4IOA image
Deposition Date 2013-01-07
Release Date 2013-03-06
Last Version Date 2024-10-30
Entry Detail
PDB ID:
4IOA
Keywords:
RIBOSOME/RIBOSOME INHIBITOR
Title:
Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans
Biological Source:
Source Organism:
Deinococcus radiodurans (Taxon ID: 1299)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
3.20 Å
R-Value Free:
0.22
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
I 2 2 2
4IOA validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:AA (auth: 1)
Chain Length:55
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RSS4 Pfam ID:PF00471
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:BA (auth: 2)
Chain Length:47
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RSH2 Pfam ID:PF00468
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:CA (auth: 3)
Chain Length:66
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RSW6 Pfam ID:PF01632
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:DA (auth: 4)
Chain Length:37
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RSK0 Pfam ID:PF00444
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:C (auth: A)
Chain Length:274
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RXJ9 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:D (auth: B)
Chain Length:211
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RXK2 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:E (auth: C)
Chain Length:205
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RXK1 Pfam ID:PF00573
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:F (auth: D)
Chain Length:180
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RXJ0 Pfam ID:PF00281, PF00673
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:G (auth: E)
Chain Length:185
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RSL3 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Gene (Uniprot):rplK
Chain IDs:H (auth: F)
Chain Length:144
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RSS7 Pfam ID:PF03946, PF00298
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:I (auth: G)
Chain Length:174
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RXY1 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:J (auth: H)
Chain Length:134
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RXJ2 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:K (auth: I)
Chain Length:156
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RSK9 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:L (auth: J)
Chain Length:141
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RXJ5 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:M (auth: K)
Chain Length:116
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RSJ5 Pfam ID:PF01196
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:N (auth: L)
Chain Length:114
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RSL2 Pfam ID:PF00861
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:O (auth: M)
Chain Length:166
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RWB4 Pfam ID:PF01245
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:P (auth: N)
Chain Length:118
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RSW7 Pfam ID:PF00453
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:Q (auth: O)
Chain Length:100
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RY64 Pfam ID:PF00829
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:R (auth: P)
Chain Length:134
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RXJ7 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:S (auth: Q)
Chain Length:95
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RXK0 Pfam ID:PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:T (auth: R)
Chain Length:115
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RXJ1 Pfam ID:PF00467, PF17136
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:U (auth: S)
Chain Length:237
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RX88 Pfam ID:PF01386, PF14693
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:V (auth: T)
Chain Length:91
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RY65 Pfam ID:PF01016
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:W (auth: U)
Chain Length:81
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RRG8 Pfam ID:PF00830
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:X (auth: V)
Chain Length:67
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RXJ4 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:Y (auth: W)
Chain Length:55
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:Q9RSL0 Pfam ID:PF00327
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:A (auth: X)
Chain Length:2880
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:B (auth: Y)
Chain Length:123
Number of Molecules:1
Biological Source:Deinococcus radiodurans
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:Z
Chain Length:60
Number of Molecules:1
Biological Source:Deinococcus radiodurans
UniProt ID:P49228 Pfam ID:PF01783
Ligand Molecules
1F3
MG
Primary Citation
Novel 3-O-carbamoyl erythromycin A derivatives (carbamolides) with activity against resistant staphylococcal and streptococcal isolates.
Bioorg.Med.Chem.Lett. 23 1727 1731 (2013)
PMID: 23414806 DOI: 10.1016/j.bmcl.2013.01.067

Abstact

A novel series of 3-O-carbamoyl erythromycin A derived analogs, labeled carbamolides, with activity versus resistant bacterial isolates of staphylococci (including macrolide and oxazolidinone resistant strains) and streptococci are reported. An (R)-2-aryl substituent on a pyrrolidine carbamate appeared to be critical for achieving potency against resistant strains. Crystal structures showed a distinct aromatic interaction between the (R)-2-aryl (3-pyridyl for 4d) substituent on the pyrrolidine and G2484 (G2505, Escherichia coli) of the Deinococcus radiodurans 50S ribosome (3.2Å resolution).

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Protein

Chemical

Disease

Primary Citation of related structures
4IO9
4IOC