data_1QA4

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  1QA4
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   nmr
#
_pdbx_vrpt_summary.entry_id                    1QA4
_pdbx_vrpt_summary.PDB_deposition_date         1999-04-12
_pdbx_vrpt_summary.PDB_revision_number         5
_pdbx_vrpt_summary.PDB_revision_date           2021-10-27
_pdbx_vrpt_summary.report_creation_date        2022-08-20:12:03
_pdbx_vrpt_summary.attempted_validation_steps  molprobity,validation-pack,coreclust,chemicalshifts,percentiles,writepdf,writexml,writecif
_pdbx_vrpt_summary.ligands_for_buster_report   N
#
_pdbx_vrpt_entity.id           1
_pdbx_vrpt_entity.type         polymer
_pdbx_vrpt_entity.description  "Protein Nef"
#
_pdbx_vrpt_asym.label_asym_id  A
_pdbx_vrpt_asym.entity_id      1
#
loop_
_pdbx_vrpt_summary_entity_geometry.ordinal
_pdbx_vrpt_summary_entity_geometry.PDB_model_num
_pdbx_vrpt_summary_entity_geometry.entity_id
_pdbx_vrpt_summary_entity_geometry.label_asym_id
_pdbx_vrpt_summary_entity_geometry.auth_asym_id
_pdbx_vrpt_summary_entity_geometry.angles_RMSZ
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ
1  1  1  A  A  0.31  0.25  415  561  
2  2  1  A  A  0.34  0.27  415  561  
#
_pdbx_vrpt_summary_geometry.ordinal                                    1
_pdbx_vrpt_summary_geometry.percent_ramachandran_outliers_full_length  4.55
_pdbx_vrpt_summary_geometry.percent_rotamer_outliers_full_length       36.84
_pdbx_vrpt_summary_geometry.clashscore_full_length                     1.88
_pdbx_vrpt_summary_geometry.num_H_reduce                               784
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ                             830
_pdbx_vrpt_summary_geometry.bonds_RMSZ                                 0.26
_pdbx_vrpt_summary_geometry.num_angles_RMSZ                            1122
_pdbx_vrpt_summary_geometry.angles_RMSZ                                0.32
#
loop_
_pdbx_vrpt_model_instance.id
_pdbx_vrpt_model_instance.PDB_model_num
_pdbx_vrpt_model_instance.entity_id
_pdbx_vrpt_model_instance.label_asym_id
_pdbx_vrpt_model_instance.label_seq_id
_pdbx_vrpt_model_instance.label_comp_id
_pdbx_vrpt_model_instance.auth_asym_id
_pdbx_vrpt_model_instance.auth_seq_id
_pdbx_vrpt_model_instance.label_alt_id
_pdbx_vrpt_model_instance.PDB_ins_code
_pdbx_vrpt_model_instance.count_clashes
  1  1  1  A   1  GLY  A   2  .  ?        ?  
  2  1  1  A   2  GLY  A   3  .  ?        ?  
  3  1  1  A   3  LYS  A   4  .  ?        ?  
  4  1  1  A   4  TRP  A   5  .  ?        ?  
  5  1  1  A   5  SER  A   6  .  ?        ?  
  6  1  1  A   6  LYS  A   7  .  ?        ?  
  7  1  1  A   7  SER  A   8  .  ?        ?  
  8  1  1  A   8  SER  A   9  .  ?        ?  
  9  1  1  A   9  VAL  A  10  .  ?        ?  
 10  1  1  A  10  VAL  A  11  .  ?        ?  
 11  1  1  A  11  GLY  A  12  .  ?        ?  
 12  1  1  A  12  TRP  A  13  .  ?        1  
 13  1  1  A  13  PRO  A  14  .  ?        ?  
 14  1  1  A  14  ALA  A  15  .  ?        1  
 15  1  1  A  15  VAL  A  16  .  ?        ?  
 16  1  1  A  16  ARG  A  17  .  ?        ?  
 17  1  1  A  17  GLU  A  18  .  ?        ?  
 18  1  1  A  18  ARG  A  19  .  ?        ?  
 19  1  1  A  19  MET  A  20  .  ?        ?  
 20  1  1  A  20  ARG  A  21  .  ?        ?  
 21  1  1  A  21  ARG  A  22  .  ?        ?  
 22  1  1  A  22  ALA  A  23  .  ?        ?  
 23  1  1  A  23  GLU  A  24  .  ?        ?  
 24  1  1  A  24  PRO  A  25  .  ?        ?  
 25  1  1  A  25  ALA  A  26  .  ?        ?  
 26  1  1  A  26  ALA  A  27  .  ?        ?  
 27  1  1  A  27  ASP  A  28  .  ?        ?  
 28  1  1  A  28  GLY  A  29  .  ?        ?  
 29  1  1  A  29  VAL  A  30  .  ?        ?  
 30  1  1  A  30  GLY  A  31  .  ?        ?  
 31  1  1  A  31  ALA  A  32  .  ?        ?  
 32  1  1  A  32  ALA  A  33  .  ?        ?  
 33  1  1  A  33  SER  A  34  .  ?        ?  
 34  1  1  A  34  ARG  A  35  .  ?        ?  
 35  1  1  A  35  ASP  A  36  .  ?        ?  
 36  1  1  A  36  LEU  A  37  .  ?        ?  
 37  1  1  A  37  GLU  A  38  .  ?        ?  
 38  1  1  A  38  LYS  A  39  .  ?        ?  
 39  1  1  A  39  HIS  A  40  .  ?        ?  
 40  1  1  A  40  GLY  A  41  .  ?        ?  
 41  1  1  A  41  ALA  A  42  .  ?        ?  
 42  1  1  A  42  ILE  A  43  .  ?        ?  
 43  1  1  A  43  THR  A  44  .  ?        ?  
 44  1  1  A  44  SER  A  45  .  ?        ?  
 45  1  1  A  45  SER  A  46  .  ?        ?  
 46  1  1  A  46  ASN  A  47  .  ?        ?  
 47  1  1  A  47  THR  A  48  .  ?        ?  
 48  1  1  A  48  ALA  A  49  .  ?        ?  
 49  1  1  A  49  ALA  A  50  .  ?        ?  
 50  1  1  A  50  ASN  A  51  .  ?        ?  
 51  1  1  A  51  ASN  A  52  .  ?        ?  
 52  1  1  A  52  ALA  A  53  .  ?        ?  
 53  1  1  A  53  ALA  A  54  .  ?        ?  
 54  1  1  A  54  CYS  A  55  .  ?        ?  
 55  1  1  A  55  ALA  A  56  .  ?        ?  
 56  1  1  A  56  TRP  A  57  .  ?        ?  
 57  1  1  A  57  NH2  A  58  .  ?        ?  
 58  2  1  A   1  GLY  A   2  .  ?        ?  
 59  2  1  A   2  GLY  A   3  .  ?        ?  
 60  2  1  A   3  LYS  A   4  .  ?        ?  
 61  2  1  A   4  TRP  A   5  .  ?        ?  
 62  2  1  A   5  SER  A   6  .  ?        ?  
 63  2  1  A   6  LYS  A   7  .  ?        ?  
 64  2  1  A   7  SER  A   8  .  ?        ?  
 65  2  1  A   8  SER  A   9  .  ?        ?  
 66  2  1  A   9  VAL  A  10  .  ?        ?  
 67  2  1  A  10  VAL  A  11  .  ?        ?  
 68  2  1  A  11  GLY  A  12  .  ?        ?  
 69  2  1  A  12  TRP  A  13  .  ?        ?  
 70  2  1  A  13  PRO  A  14  .  ?        ?  
 71  2  1  A  14  ALA  A  15  .  ?        ?  
 72  2  1  A  15  VAL  A  16  .  ?        ?  
 73  2  1  A  16  ARG  A  17  .  ?        ?  
 74  2  1  A  17  GLU  A  18  .  ?        ?  
 75  2  1  A  18  ARG  A  19  .  ?        ?  
 76  2  1  A  19  MET  A  20  .  ?        ?  
 77  2  1  A  20  ARG  A  21  .  ?        ?  
 78  2  1  A  21  ARG  A  22  .  ?        ?  
 79  2  1  A  22  ALA  A  23  .  ?        ?  
 80  2  1  A  23  GLU  A  24  .  ?        ?  
 81  2  1  A  24  PRO  A  25  .  ?        ?  
 82  2  1  A  25  ALA  A  26  .  ?        ?  
 83  2  1  A  26  ALA  A  27  .  ?        ?  
 84  2  1  A  27  ASP  A  28  .  ?        ?  
 85  2  1  A  28  GLY  A  29  .  ?        ?  
 86  2  1  A  29  VAL  A  30  .  ?        ?  
 87  2  1  A  30  GLY  A  31  .  ?        ?  
 88  2  1  A  31  ALA  A  32  .  ?        ?  
 89  2  1  A  32  ALA  A  33  .  ?        ?  
 90  2  1  A  33  SER  A  34  .  ?        2  
 91  2  1  A  34  ARG  A  35  .  ?        ?  
 92  2  1  A  35  ASP  A  36  .  ?        ?  
 93  2  1  A  36  LEU  A  37  .  ?        ?  
 94  2  1  A  37  GLU  A  38  .  ?        1  
 95  2  1  A  38  LYS  A  39  .  ?        1  
 96  2  1  A  39  HIS  A  40  .  ?        ?  
 97  2  1  A  40  GLY  A  41  .  ?        ?  
 98  2  1  A  41  ALA  A  42  .  ?        ?  
 99  2  1  A  42  ILE  A  43  .  ?        ?  
100  2  1  A  43  THR  A  44  .  ?        ?  
101  2  1  A  44  SER  A  45  .  ?        ?  
102  2  1  A  45  SER  A  46  .  ?        ?  
103  2  1  A  46  ASN  A  47  .  ?        ?  
104  2  1  A  47  THR  A  48  .  ?        ?  
105  2  1  A  48  ALA  A  49  .  ?        ?  
106  2  1  A  49  ALA  A  50  .  ?        ?  
107  2  1  A  50  ASN  A  51  .  ?        ?  
108  2  1  A  51  ASN  A  52  .  ?        ?  
109  2  1  A  52  ALA  A  53  .  ?        ?  
110  2  1  A  53  ALA  A  54  .  ?        ?  
111  2  1  A  54  CYS  A  55  .  ?        ?  
112  2  1  A  55  ALA  A  56  .  ?        ?  
113  2  1  A  56  TRP  A  57  .  ?        ?  
114  2  1  A  57  NH2  A  58  .  ?        ?  
#
loop_
_pdbx_vrpt_model_instance_geometry.ordinal
_pdbx_vrpt_model_instance_geometry.instance_id
_pdbx_vrpt_model_instance_geometry.rotamer_class
_pdbx_vrpt_model_instance_geometry.phi
_pdbx_vrpt_model_instance_geometry.psi
_pdbx_vrpt_model_instance_geometry.ramachandran_class
_pdbx_vrpt_model_instance_geometry.num_H_reduce
_pdbx_vrpt_model_instance_geometry.num_bonds_RMSZ
_pdbx_vrpt_model_instance_geometry.bonds_RMSZ
_pdbx_vrpt_model_instance_geometry.num_angles_RMSZ
_pdbx_vrpt_model_instance_geometry.angles_RMSZ
_pdbx_vrpt_model_instance_geometry.program_for_bond_angle_geometry
  1    1  ?             ?       ?  ?         2   4  1.20   5  0.33  molprobity  
  2    2  ?        -154.1   130.2  Favored   3   4  0.15   5  0.21  molprobity  
  3    3  OUTLIER  -154.2    95.1  Allowed  13   9  0.24  11  0.20  molprobity  
  4    4  m-90     -139.9   141.0  Favored  10  16  0.13  23  0.17  molprobity  
  5    5  t         -79.5    97.7  Favored   5   6  0.24   8  0.23  molprobity  
  6    6  OUTLIER  -119.7   112.3  Favored  13   9  0.22  11  0.22  molprobity  
  7    7  t        -143.7   137.4  Favored   5   6  0.20   8  0.21  molprobity  
  8    8  p        -149.1   128.6  Favored   5   6  0.26   8  0.22  molprobity  
  9    9  p        -128.1   146.6  Favored   9   7  0.16  10  0.37  molprobity  
 10   10  t        -118.1   137.1  Favored   9   7  0.20  10  0.44  molprobity  
 11   11  ?        -154.2   111.9  Allowed   3   4  0.18   5  0.21  molprobity  
 12   12  p-90     -145.5   147.6  Favored  10  16  0.21  24  0.34  molprobity  
 13   13  Cg_endo   -74.1   136.3  Favored   7   8  0.19  11  0.27  molprobity  
 14   14  ?        -158.0   127.1  Favored   5   5  0.16   7  0.18  molprobity  
 15   15  p        -128.2   -56.3  Allowed   9   7  0.22  10  0.30  molprobity  
 16   16  OUTLIER   177.8   152.1  Allowed  13  11  0.28  14  0.40  molprobity  
 17   17  OUTLIER  -155.3   136.1  Favored   6   9  0.26  12  0.21  molprobity  
 18   18  OUTLIER  -132.1    84.8  Favored  13  11  0.29  14  0.55  molprobity  
 19   19  OUTLIER   -97.5   129.1  Favored   9   8  0.20  10  0.25  molprobity  
 20   20  OUTLIER  -150.9   122.9  Favored  13  11  0.25  14  0.44  molprobity  
 21   21  OUTLIER  -149.5  -172.7  Favored  13  11  0.23  14  0.33  molprobity  
 22   22  ?          64.9    53.8  Allowed   5   5  0.24   7  0.41  molprobity  
 23   23  pm0       -95.5   133.6  Favored   6   9  0.30  13  0.47  molprobity  
 24   24  Cg_endo   -71.8   114.1  Favored   7   8  0.17  11  0.24  molprobity  
 25   25  ?         -80.2   136.4  Favored   5   5  0.13   7  0.24  molprobity  
 26   26  ?         -93.1   126.5  Favored   5   5  0.14   7  0.26  molprobity  
 27   27  OUTLIER  -100.5   173.6  Favored   4   8  0.22  11  0.26  molprobity  
 28   28  ?         102.4   -93.7  Allowed   3   4  0.12   5  0.22  molprobity  
 29   29  m        -143.1   107.8  Allowed   9   7  0.21  10  0.44  molprobity  
 30   30  ?        -132.2    58.0  Allowed   3   4  0.12   5  0.21  molprobity  
 31   31  ?        -149.8   147.4  Favored   5   5  0.16   7  0.25  molprobity  
 32   32  ?         -71.6   136.9  Favored   5   5  0.15   7  0.27  molprobity  
 33   33  OUTLIER   -71.2    76.4  Allowed   5   6  0.32   8  0.24  molprobity  
 34   34  OUTLIER   -72.3   -57.5  Favored  13  11  0.24  14  0.33  molprobity  
 35   35  OUTLIER   -59.8   -35.9  Favored   4   8  0.13  11  0.19  molprobity  
 36   36  OUTLIER   -50.6   -37.4  Favored  11   8  0.22  11  0.18  molprobity  
 37   37  OUTLIER   -66.8   -47.8  Favored   6   9  0.27  12  0.33  molprobity  
 38   38  OUTLIER   -67.2   -44.5  Favored  13   9  0.24  11  0.18  molprobity  
 39   39  m-70      -72.5   -39.9  Favored   7  11  0.17  15  0.22  molprobity  
 40   40  ?         -72.2   -36.5  Favored   3   4  0.20   5  0.12  molprobity  
 41   41  ?         -96.2    39.8  Allowed   5   5  0.25   7  0.23  molprobity  
 42   42  tp       -123.0   -37.8  Allowed  11   8  0.21  11  0.37  molprobity  
 43   43  p        -122.9   164.4  Favored   7   7  0.28  10  0.56  molprobity  
 44   44  t        -108.6   -51.4  Favored   5   6  0.27   8  0.16  molprobity  
 45   45  t        -115.0    89.5  Favored   5   6  0.24   8  0.24  molprobity  
 46   46  OUTLIER  -101.9   125.6  Favored   6   8  0.23  11  0.29  molprobity  
 47   47  m          58.9    55.0  Favored   7   7  0.33  10  0.55  molprobity  
 48   48  ?         -98.5   142.1  Favored   5   5  0.15   7  0.25  molprobity  
 49   49  ?         -79.9   151.6  Favored   5   5  0.14   7  0.35  molprobity  
 50   50  p30        48.2  -163.3  OUTLIER   6   8  0.42  11  0.24  molprobity  
 51   51  OUTLIER  -141.8   166.4  Favored   6   8  0.24  11  0.29  molprobity  
 52   52  ?         -70.0   140.0  Favored   5   5  0.15   7  0.31  molprobity  
 53   53  ?          73.0   152.4  Allowed   5   5  0.23   7  0.34  molprobity  
 54   54  p        -145.0   154.7  Favored   5   6  0.18   8  0.23  molprobity  
 55   55  ?         -89.2   149.5  Favored   5   5  0.14   7  0.30  molprobity  
 56   56  m95        68.9   -80.0  OUTLIER  10  15  0.16  20  0.14  molprobity  
 57   58  ?             ?       ?  ?         2   4  1.20   5  0.30  molprobity  
 58   59  ?          91.0  -145.5  Favored   3   4  0.14   5  0.30  molprobity  
 59   60  OUTLIER    55.9    56.5  Favored  13   9  0.26  11  0.24  molprobity  
 60   61  m-90     -106.9   177.6  Favored  10  16  0.13  23  0.17  molprobity  
 61   62  t          65.3    55.2  Allowed   5   6  0.32   8  0.25  molprobity  
 62   63  pptp?    -158.4   134.5  Favored  13   9  0.23  11  0.21  molprobity  
 63   64  t        -146.8   151.2  Favored   5   6  0.23   8  0.23  molprobity  
 64   65  p         -90.5   119.8  Favored   5   6  0.29   8  0.20  molprobity  
 65   66  p         -97.5   150.7  Favored   9   7  0.16  10  0.42  molprobity  
 66   67  OUTLIER    72.5   158.1  OUTLIER   9   7  0.34  10  0.42  molprobity  
 67   68  ?        -139.9   174.2  Favored   3   4  0.18   5  0.22  molprobity  
 68   69  p90      -155.2   152.9  Favored  10  16  0.21  24  0.34  molprobity  
 69   70  Cg_endo   -72.5   166.9  Favored   7   8  0.18  11  0.26  molprobity  
 70   71  ?        -105.3    51.5  Allowed   5   5  0.18   7  0.34  molprobity  
 71   72  t          71.0   -66.8  Allowed   9   7  0.23  10  0.40  molprobity  
 72   73  OUTLIER    80.3   -45.5  Allowed  13  11  0.35  14  0.48  molprobity  
 73   74  OUTLIER   -42.5   -54.5  Favored   6   9  0.27  12  0.23  molprobity  
 74   75  OUTLIER   -82.8    68.8  Favored  13  11  0.30  14  0.47  molprobity  
 75   76  ppp?     -105.1   -37.5  Favored   9   8  0.26  10  0.27  molprobity  
 76   77  tmm_?     -75.3   113.3  Favored  13  11  0.26  14  0.50  molprobity  
 77   78  OUTLIER   -74.3   -47.9  Favored  13  11  0.25  14  0.43  molprobity  
 78   79  ?         -62.6   121.5  Favored   5   5  0.17   7  0.28  molprobity  
 79   80  OUTLIER  -128.3   132.3  Favored   6   9  0.30  13  0.46  molprobity  
 80   81  Cg_endo   -74.1    67.9  Favored   7   8  0.24  11  0.26  molprobity  
 81   82  ?        -131.0   131.2  Favored   5   5  0.13   7  0.24  molprobity  
 82   83  ?        -120.1   107.5  Favored   5   5  0.14   7  0.30  molprobity  
 83   84  OUTLIER    64.7  -178.0  Allowed   4   8  0.27  11  0.28  molprobity  
 84   85  ?         166.9   -72.0  Allowed   3   4  0.17   5  0.25  molprobity  
 85   86  m        -145.4   163.4  Favored   9   7  0.22  10  0.46  molprobity  
 86   87  ?         -66.8   108.0  Favored   3   4  0.14   5  0.25  molprobity  
 87   88  ?         -75.6    75.3  Favored   5   5  0.17   7  0.31  molprobity  
 88   89  ?         -86.0   -66.2  Allowed   5   5  0.14   7  0.25  molprobity  
 89   90  p         -76.7    94.7  Favored   5   6  0.28   8  0.20  molprobity  
 90   91  OUTLIER   -82.5   -82.4  Allowed  13  11  0.33  14  0.66  molprobity  
 91   92  m-20      -95.3   -72.5  Allowed   4   8  0.24  11  0.35  molprobity  
 92   93  OUTLIER   -70.9   -56.4  Favored  11   8  0.21  11  0.27  molprobity  
 93   94  tt0       -48.7   -38.5  Favored   6   9  0.24  12  0.32  molprobity  
 94   95  OUTLIER   -58.0   -56.5  Favored  13   9  0.23  11  0.21  molprobity  
 95   96  m170      -74.9   -38.7  Favored   7  11  0.21  15  0.21  molprobity  
 96   97  ?         -59.6   -46.1  Favored   3   4  0.16   5  0.16  molprobity  
 97   98  ?         -82.7    51.3  Allowed   5   5  0.24   7  0.27  molprobity  
 98   99  mm       -125.7   105.1  Favored  11   8  0.16  11  0.42  molprobity  
 99  100  m        -103.0    82.7  Favored   7   7  0.28  10  0.54  molprobity  
100  101  t        -131.0   105.2  Favored   5   6  0.22   8  0.20  molprobity  
101  102  m        -132.5   148.5  Favored   5   6  0.22   8  0.21  molprobity  
102  103  t30      -103.4   132.9  Favored   6   8  0.24  11  0.25  molprobity  
103  104  p        -107.7    98.4  Favored   7   7  0.27  10  0.58  molprobity  
104  105  ?          62.4  -174.5  Allowed   5   5  0.25   7  0.28  molprobity  
105  106  ?          63.8  -172.8  Allowed   5   5  0.27   7  0.27  molprobity  
106  107  p30      -141.0   130.6  Favored   6   8  0.26  11  0.25  molprobity  
107  108  t-20       64.8  -178.4  Allowed   6   8  0.28  11  0.27  molprobity  
108  109  ?         -80.4    77.7  Favored   5   5  0.16   7  0.43  molprobity  
109  110  ?          67.7   -84.1  OUTLIER   5   5  0.25   7  0.37  molprobity  
110  111  t          53.3    39.4  Favored   5   6  0.27   8  0.22  molprobity  
111  112  ?        -169.5   144.3  Favored   5   5  0.19   7  0.27  molprobity  
112  113  t90        68.7   140.4  OUTLIER  10  15  0.19  20  0.17  molprobity  
#
loop_
_pdbx_vrpt_instance_clashes.ordinal
_pdbx_vrpt_instance_clashes.instance_id
_pdbx_vrpt_instance_clashes.label_atom_id
_pdbx_vrpt_instance_clashes.cid
_pdbx_vrpt_instance_clashes.clashmag
_pdbx_vrpt_instance_clashes.dist
1  12  CZ3  1  0.43  2.48  
2  14  HB2  1  0.43  2.48  
3  90  HA   2  0.55  1.77  
4  90  HB2  3  0.47  2.25  
5  94  HB3  2  0.55  1.77  
6  95  N    3  0.47  2.25  
#
loop_
_pdbx_vrpt_software.ordinal
_pdbx_vrpt_software.name
_pdbx_vrpt_software.version
_pdbx_vrpt_software.success_y_or_n
1  molprobity   4.02b-467                                                             Y  
2  mogul        unknown                                                               Y  
3  percentiles  "20191225.v01 (using entries in the PDB archive December 25th 2019)"  N  
##
