Research workbench
The crystal structure of S. aureus gyrase complex with id-130 and DNA
Analyse The crystal structure of S. aureus gyrase complex with id-130 and DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FM4
- Type
- protein + DNA
- Length
- 1,379 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit a; DNA (5'…
- EC
- 5.99.1.3
- UniProt
- P66937, Q99XG5
- Ligands
- 5UA, DU5, MN
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit a (EC 5.99.1.3) | protein | 672 | 48% helix, 15% strand | P66937, Q99XG5 |
| D | DNA gyrase subunit B,DNA gyrase subunit B,DNA gyrase subunit a (EC 5.99.1.3) | protein | 670 | 49% helix, 16% strand | P66937, Q99XG5 |
| E | DNA (5'- 5UA*D(P*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3') | dna | 19 | — | — |
| F | DNA (5'- 5UA*D(P*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP*GP*C)-3') | dna | 18 | — | — |
Ligands and binding sites
- 5UA · 5'-O-carboxy-2'-deoxyadenosine · ligand · 2 copies · chains E, F, D
- DU5 · ~{N}-[3-(4-isoquinolin-1-ylpiperazin-1-yl) propyl]benzamide · ligand · chains B, D, E, F
- MN · Manganese (II) ion · metal · 3 copies · chains B, E, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1013 | 0.84 | 0.85 | 112 | DU5 |
| 2 | 414 | 0.73 | 0.84 | 31 | empty |
| 3 | 52 | 0.69 | 0.98 | 23 | empty |
| 4 | 307 | 0.67 | 0.82 | 29 | empty |
| 5 | 505 | 0.65 | 0.77 | 58 | empty |
Interfaces
6 interfaces between chains.
- B–D · 3183 Ų buried · 58 hydrogen bonds · protein-protein
- B–E · 992 Ų buried · 23 hydrogen bonds · protein-nucleic
- D–F · 959 Ų buried · 23 hydrogen bonds · protein-nucleic
- E–F · 869 Ų buried · 92 hydrogen bonds · nucleic-nucleic
- D–E · 851 Ų buried · 18 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6FM4 · The crystal structure of S. aureus Gyrase complex with ID-130 and DNA · the same entry in another collection · chain F against F, TM-score 1.00
- Q99XG5 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit a (Q99XG5) · a predicted model of the same protein · chain B against A, TM-score 0.72
- P66937 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (P66937) · a predicted model of the same protein · chain D 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 P66937
- Every structure of UniProt Q99XG5
- Elsewhere: RCSB PDB 6FM4 · PDBe 6FM4 · UniProt P66937 · UniProt Q99XG5
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