4v7l

X-ray diffraction
3Å resolution

The structures of viomycin bound to the 70S ribosome.

Released:
Model geometry
Fit model/data

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 58-mer (preferred)
PDBe Complex ID:
PDB-CPX-294053 (preferred)
Entry contents:
51 distinct polypeptide molecules
7 distinct RNA molecules
Macromolecules (58 distinct):
Small ribosomal subunit protein uS2 Chains: AB, CB
Molecule details ›
Chains: AB, CB
Length: 256 amino acids
Theoretical weight: 29.32 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80371 (Residues: 1-256; Coverage: 100%)
Gene names: TTHA0861, rps2, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chains: AC, CC
Molecule details ›
Chains: AC, CC
Length: 239 amino acids
Theoretical weight: 26.75 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80372 (Residues: 1-239; Coverage: 100%)
Gene names: TTHA1686, rps3, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chains: AD, CD
Small ribosomal subunit protein uS5 Chains: AE, CE
Small ribosomal subunit protein bS6 Chains: AF, CF
Small ribosomal subunit protein uS7 Chains: AG, CG
30S ribosomal protein S8 Chains: AH, CH
Small ribosomal subunit protein uS9 Chains: AI, CI
Small ribosomal subunit protein uS10 Chains: AJ, CJ
Small ribosomal subunit protein uS11 Chains: AK, CK
Small ribosomal subunit protein uS12 Chains: AL, CL
Small ribosomal subunit protein uS13 Chains: AM, CM
30S ribosomal protein S14 Chains: AN, CN
Small ribosomal subunit protein uS15 Chains: AO, CO
Small ribosomal subunit protein bS16 Chains: AP, CP
30S ribosomal protein S17 Chains: AQ, CQ
Small ribosomal subunit protein bS18 Chains: AR, CR
Small ribosomal subunit protein uS19 Chains: AS, CS
Small ribosomal subunit protein bS20 Chains: AT, CT
Small ribosomal subunit protein bTHX Chains: AU, CU
Viomycin Chains: AZ, CZ
Large ribosomal subunit protein uL1 Chains: BC, DC
Large ribosomal subunit protein uL2 Chains: BD, DD
Large ribosomal subunit protein uL3 Chains: BE, DE
Large ribosomal subunit protein uL4 Chains: BF, DF
Large ribosomal subunit protein uL5 Chains: BG, DG
50S ribosomal protein L6 Chains: BH, DH
Large ribosomal subunit protein bL9 Chains: BI, DI
Large ribosomal subunit protein uL13 Chains: BN, DN
Large ribosomal subunit protein uL14 Chains: BO, DO
Large ribosomal subunit protein uL15 Chains: BP, DP
Large ribosomal subunit protein uL16 Chains: BQ, DQ
Large ribosomal subunit protein bL17 Chains: BR, DR
Large ribosomal subunit protein uL18 Chains: BS, DS
Large ribosomal subunit protein bL19 Chains: BT, DT
Large ribosomal subunit protein bL20 Chains: BU, DU
Large ribosomal subunit protein bL21 Chains: BV, DV
Large ribosomal subunit protein uL22 Chains: BW, DW
Large ribosomal subunit protein uL23 Chains: BX, DX
Large ribosomal subunit protein uL24 Chains: BY, DY
Large ribosomal subunit protein bL25 Chains: BZ, DZ
Large ribosomal subunit protein bL27 Chains: B0, D0
Large ribosomal subunit protein bL28 Chains: B1, D1
Large ribosomal subunit protein uL29 Chains: B2, D2
Large ribosomal subunit protein uL30 Chains: B3, D3
Large ribosomal subunit protein bL31 Chains: B4, D4
Large ribosomal subunit protein bL32 Chains: B5, D5
Large ribosomal subunit protein bL33 Chains: B6, D6
Large ribosomal subunit protein bL34 Chains: B7, D7
Large ribosomal subunit protein bL35 Chains: B8, D8
Large ribosomal subunit protein bL36 Chains: B9, D9
16S ribosomal RNA Chains: AA, CA
RNA (5'-R(*AP*AP*AP*AP*AP*GP*GP*AP*AP*AP*UP*A*AP*AP*AP*AP*UP*GP*CP*AP*GP*UP*UP*CP*AP*AP*UP*CP*UP*A)-3') Chains: AV, CV
tRNA-Gln Chains: AW, CW
tRNA-Met Chains: AX, CX
tRNA-Gln Chains: AY, CY
23S ribosomal RNA Chains: BA, DA
5S ribosomal RNA Chains: BB, DB

Ligands and Environments

2 bound ligands:
3 modified residues:

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 210.23Å b: 448.51Å c: 633.62Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.248 0.248 0.272