2F4V image
Deposition Date 2005-11-24
Release Date 2006-07-04
Last Version Date 2024-10-16
Entry Detail
PDB ID:
2F4V
Keywords:
RIBOSOME
Title:
30S ribosome + designer antibiotic
Biological Source:
Source Organism:
Thermus thermophilus (Taxon ID: 274)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
3.80 Å
R-Value Free:
0.31
R-Value Work:
0.25
R-Value Observed:
0.26
Space Group:
P 41 21 2
2F4V validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:A
Chain Length:1511
Number of Molecules:1
Biological Source:Thermus thermophilus
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:C (auth: B)
Chain Length:256
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80371 Pfam ID:PF00318
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:D (auth: C)
Chain Length:239
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80372 Pfam ID:PF07650, PF00189
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:E (auth: D)
Chain Length:209
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80373 Pfam ID:PF00163, PF01479
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Chain IDs:F (auth: E)
Chain Length:162
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHQ5 Pfam ID:PF00333, PF03719
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Chain IDs:G (auth: F)
Chain Length:101
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SLP8 Pfam ID:PF01250
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:H (auth: G)
Chain Length:156
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P17291 Pfam ID:PF00177
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Chain IDs:I (auth: H)
Chain Length:138
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P0DOY9 Pfam ID:PF00410
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Chain IDs:J (auth: I)
Chain Length:128
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80374 Pfam ID:PF00380
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Chain IDs:K (auth: J)
Chain Length:105
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHN7 Pfam ID:PF00338
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:L (auth: K)
Chain Length:129
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80376 Pfam ID:PF00411
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Chain IDs:M (auth: L)
Chain Length:132
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHN3 Pfam ID:PF00164
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:N (auth: M)
Chain Length:126
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80377 Pfam ID:PF00416
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Chain IDs:O (auth: N)
Chain Length:61
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P0DOY6 Pfam ID:PF00253
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Chain IDs:P (auth: O)
Chain Length:89
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SJ76 Pfam ID:PF00312
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:Q (auth: P)
Chain Length:88
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SJH3 Pfam ID:PF00886
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Chain IDs:R (auth: Q)
Chain Length:105
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P0DOY7 Pfam ID:PF00366
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Chain IDs:S (auth: R)
Chain Length:88
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SLQ0 Pfam ID:PF01084
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Chain IDs:T (auth: S)
Chain Length:93
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHP2 Pfam ID:PF00203
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Chain IDs:U (auth: T)
Chain Length:106
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80380 Pfam ID:PF01649
Polymer Type:polyribonucleotide
Molecule:5'-R(P*UP*UP*CP*U)-3'
Chain IDs:B (auth: Z)
Chain Length:4
Number of Molecules:1
Biological Source:Thermus thermophilus
Ligand Molecules
AB9
D2C
K
MG
ZN
Primary Citation
Interactions of designer antibiotics and the bacterial ribosome aminoacyl-tRNA site
Chem.Biol. 13 129 138 (2006)
PMID: 16492561 DOI: 10.1016/j.chembiol.2005.11.004

Abstact

The X-ray crystal structures for the complexes of three designer antibiotics, compounds 1, 2, and 3, bound to two models for the ribosomal aminoacyl-tRNA site (A site) at 2.5-3.0 Angstroms resolution and that of neamine at 2.8 Angstroms resolution are described. Furthermore, the complex of antibiotic 1 bound to the A site in the entire 30S ribosomal subunit of Thermus thermophilus is reported at 3.8 Angstroms resolution. Molecular dynamics simulations revealed that the designer compounds provide additional stability to bases A1492 and A1493 in their extrahelical forms. Snapshots from the simulations were used for free energy calculations, which revealed that van der Waals and hydrophobic effects were the driving forces behind the binding of designer antibiotic 3 when compared to the parental neamine.

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Protein

Chemical

Disease

Primary Citation of related structures
2F4S
2F4T
2F4U