MolNFT v1 · #149119 · protein + DNA
3.11A complex of S.AUREUS gyrase with imidazopyrazinone T3 and DNA
6FQS · DNA gyrase subunit B,DNA gyrase subunit B: “3.11A complex of S.AUREUS gyrase with imidazopyrazinone T3 and DNA”. X-ray diffraction, 4 ligands (E3E, MN, NA), 16 pockets (best druggability 0.80). MolNFT v1 #149119 on GenesisL1: 3D…
- PDB
- 6FQS
- Type
- protein + DNA
- Length
- 1,380 residues
- Chains
- 6
- 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
- E3E, MN, NA, SO4
- Pockets
- 16 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA gyrase subunit B,DNA gyrase subunit B (EC 5.99.1.3) | protein | 189 | 48% helix, 13% strand | P66937 |
| A, C | DNA gyrase subunit a (EC 5.99.1.3) | protein | 481 | 50% helix, 18% strand | Q99XG5 |
| D | DNA gyrase subunit B,DNA gyrase subunit B (EC 5.99.1.3) | protein | 189 | 44% helix, 13% strand | P66937 |
| E, F | DNA (5'- D(*GP*AP*GP*AP*GP*TP*AP*T*GP*GP*CP*CP*AP*TP*AP*CP*TP*CP*TP*T)-3') | dna | 20 | — | — |
Ligands and binding sites
- E3E · 5-cyclopropyl-8-fluoranyl-7-pyridin-4-yl-imidazo[1,2-a]quinoxalin-4-one · ligand · 2 copies · chains B, A, C, E, F, D
- MN · Manganese (II) ion · metal · 2 copies · chains B, D
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A, C
- GOL · Glycerol · additive · 8 copies · chains A, E, B, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 695 | 0.80 | 0.85 | 64 | MN, E3E |
| 2 | 388 | 0.78 | 0.87 | 35 | empty |
| 3 | 305 | 0.75 | 0.87 | 63 | MN, E3E |
| 4 | 236 | 0.74 | 0.89 | 43 | GOL |
| 5 | 323 | 0.69 | 0.83 | 29 | empty |
Interfaces
14 interfaces between chains.
- A–C · 1655 Ų buried · 25 hydrogen bonds · protein-protein
- D–C · 1456 Ų buried · 10 hydrogen bonds · protein-protein
- B–A · 1430 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 905 Ų buried · 78 hydrogen bonds · nucleic-nucleic
- A–E · 689 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 6FQS · 3.11A complex of S.Aureus gyrase with imidazopyrazi T3 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 A against A, TM-score 0.98
- 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 0.98
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 6FQS · PDBe 6FQS · UniProt P66937 · UniProt Q99XG5
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