MolNFT v1 · #149113 · protein + DNA
3.06A complex of S.AUREUS gyrase with imidazopyrazinone T1 and DNA
6FQM · DNA gyrase subunit B: “3.06A complex of S.AUREUS gyrase with imidazopyrazinone T1 and DNA”. X-ray diffraction, 3 ligands (E32, MN, SO4), 20 pockets (best druggability 0.80). MolNFT v1 #149113 on GenesisL1: 3D structure, binding…
- PDB
- 6FQM
- Type
- protein + DNA
- Length
- 2,611 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit B; DNA gyrase subunit a; DNA (5'…
- EC
- 5.99.1.3
- UniProt
- P66937, Q99XG5
- Ligands
- E32, MN, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 10 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA gyrase subunit B (EC 5.99.1.3) | protein | 156 | 41% helix, 15% strand | P66937 |
| A | DNA gyrase subunit a (EC 5.99.1.3) | protein | 482 | 51% helix, 18% strand | Q99XG5 |
| D | DNA gyrase subunit B (EC 5.99.1.3) | protein | 150 | 43% helix, 16% strand | P66937 |
| C | DNA gyrase subunit a (EC 5.99.1.3) | protein | 481 | 51% helix, 18% strand | Q99XG5 |
| E, e | DNA (5'- D(*GP*AP*GP*AP*GP*TP*AP*T*GP*GP*CP*CP*AP*TP*AP*CP*TP*CP*T)-3') | dna | 19 | — | — |
| F, f | DNA (5'- D(*GP*AP*GP*AP*GP*TP*AP*T*GP*GP*CP*CP*AP*TP*AP*CP*TP*CP*T)-3') | dna | 20 | — | — |
| b | DNA gyrase subunit B (EC 5.99.1.3) | protein | 160 | 40% helix, 17% strand | P66937 |
| a | DNA gyrase subunit a (EC 5.99.1.3) | protein | 474 | 51% helix, 17% strand | Q99XG5 |
| d | DNA gyrase subunit B (EC 5.99.1.3) | protein | 150 | 43% helix, 16% strand | P66937 |
| c | DNA gyrase subunit a (EC 5.99.1.3) | protein | 480 | 50% helix, 17% strand | Q99XG5 |
Ligands and binding sites
- E32 · 7-[(3~{S})-3-azanylpyrrolidin-1-yl]-5-cyclopropyl-8-fluoranyl-imidazo[1,2-a]quinoxalin-4-one · ligand · 6 copies · chains A, D, C, E, F, B, a, d, c, e, f, b
- MN · Manganese (II) ion · metal · 4 copies · chains B, D, b, d
- SO4 · Sulfate ion · ion · 2 copies · chains A, C, c
- GOL · Glycerol · additive · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1160 | 0.80 | 0.82 | 113 | E32 |
| 2 | 623 | 0.79 | 0.85 | 63 | empty |
| 3 | 459 | 0.72 | 0.82 | 35 | empty |
| 4 | 434 | 0.71 | 0.82 | 31 | empty |
| 5 | 246 | 0.68 | 0.85 | 33 | empty |
Interfaces
29 interfaces between chains.
- A–C · 1816 Ų buried · 27 hydrogen bonds · protein-protein
- a–c · 1760 Ų buried · 32 hydrogen bonds · protein-protein
- b–a · 1345 Ų buried · 9 hydrogen bonds · protein-protein
- B–A · 1278 Ų buried · 9 hydrogen bonds · protein-protein
- d–c · 1251 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 1 disulfide (phosphorylation, disulfide).
Compared structures
- 6FQM · 3.06A COMPLEX OF S.AUREUS GYRASE with imidazopyrazi T1 AND DNA · the same entry in another collection · chain f against f, TM-score 1.00
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 6FQM · PDBe 6FQM · UniProt P66937 · UniProt Q99XG5
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