Research workbench
Crystal structure of S.A. gyrase in complex with compound 7
Analyse Crystal structure of S.A. gyrase in complex with compound 7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BS3
- Type
- protein + RNA
- Length
- 1,379 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit a and B; DNA/RNA (5'-R(P*AP*GP*CP*CP*G)-D(P*T)…
- EC
- 5.99.1.3
- UniProt
- P0A0K8, P20831
- Ligands
- WCP, MN, SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | DNA gyrase subunit a and B (EC 5.99.1.3) | protein | 670 | 48% helix, 16% strand | P0A0K8, P20831 |
| E | DNA/RNA (5'-R(P*AP*GP*CP*CP*G)-D(P*T)- R(P*AP*GP*GP*GP*CP*CP*C)-D(P*T)-R(P*AP*CP*GP*GP*C)-D(P*T)-3') | rna | 20 | — | — |
| F | DNA/RNA (5'-R(P*AP*GP*CP*CP*G)-D(P*T)- R(P*AP*GP*GP*GP*CP*CP*C)-D(P*T)-R(P*AP*CP*GP*GP*C)-D(P*T)-3') | rna | 19 | — | — |
Ligands and binding sites
- WCP · (4R)-3-fluoro-4-hydroxy-4-{[(1R,4R)-4-{[(3-oxo-3,4-dihydro-2H-pyrido[3,2-b][1,4]oxazin-6-yl) methyl]amino}-2-oxabicyclo[2.2.2]oct-1-yl]methyl}-4,5-dihydro-7H-pyrrolo[3,2,1-de][1,5]naphthyridin-7-one · ligand · chains B, D, E, F
- MN · Manganese (II) ion · metal · 2 copies · chains B, E, D, F
- SO4 · Sulfate ion · ion · 3 copies · chains B, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1084 | 0.81 | 0.83 | 99 | SO4, WCP |
| 2 | 505 | 0.74 | 0.83 | 33 | empty |
| 3 | 310 | 0.68 | 0.83 | 34 | empty |
| 4 | 411 | 0.67 | 0.80 | 32 | empty |
| 5 | 390 | 0.65 | 0.79 | 46 | empty |
Interfaces
6 interfaces between chains.
- B–D · 3089 Ų buried · 46 hydrogen bonds · protein-protein
- B–E · 1007 Ų buried · 21 hydrogen bonds · protein-nucleic
- D–F · 974 Ų buried · 19 hydrogen bonds · protein-nucleic
- E–F · 927 Ų buried · 103 hydrogen bonds · nucleic-nucleic
- D–E · 840 Ų buried · 18 hydrogen bonds · protein-nucleic
Compared structures
- P20831 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit a (P20831) · a predicted model of the same protein · chain B against A, TM-score 0.72
- P0A0K8 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (P0A0K8) · a predicted model of the same protein · chain B against A, TM-score 0.28
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0A0K8
- Every structure of UniProt P20831
- Elsewhere: RCSB PDB 5BS3 · PDBe 5BS3 · UniProt P0A0K8 · UniProt P20831
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