ISDA

Deposition Date 2013-01-07

Release Date 2013-03-06

Last Version Date 2024-10-30

Entry Detail

PDB ID:

4IO9

Keywords:

RIBOSOME/RIBOSOME INHIBITOR

Title:

Crystal structure of compound 4d 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:

0.23

R-Value Work:

0.19

R-Value Observed:

0.20

Space Group:

I 2 2 2

Download 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

1F2

Primary Citation

Novel 3-O-carbamoyl erythromycin A derivatives (carbamolides) with activity against resistant staphylococcal and streptococcal isolates.

Magee, T.V, Han, S, McCurdy, S.P, Nguyen, T.T, Granskog, K, Marr, E.S, Maguire, B.A, Huband, M.D, Chen, J.M, Subashi, T.A, Shanmugasundaram, V.Show

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).

Legend

Protein

Chemical

Disease

Primary Citation of related structures