MolNFT v1 · #161932 · protein + DNA
2.31A structure of gepotidacin with S.AUREUS DNA gyrase and doubly nicked DNA
6QTK: “2.31A structure of gepotidacin with S.AUREUS DNA gyrase and doubly nicked DNA”. X-ray diffraction, 3 ligands (JHN, MN, NA). MolNFT v1 #161932 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6QTK
- Type
- protein + DNA
- Length
- 1,390 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- P66937, Q99XG5
- Ligands
- JHN, MN, NA
Structure
x-ray diffraction · 4 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | — | protein | 192 | — | P66937 |
| A | — | protein | 484 | — | Q99XG5 |
| C | — | protein | 482 | — | Q99XG5 |
| E, F | — | dna | 20 | — | — |
Ligands and binding sites
- JHN · (3~{R})-3-[[4-(3,4-dihydro-2~{H}-pyrano[2,3-c]pyridin-6-ylmethylamino)piperidin-1-yl]methyl]-1,4,7-triazatricyclo[6.3.1.0^{4,12}]dodeca-6,8(12),9-triene-5,11-dione · ligand · chains A, C, E, F
- MN · Manganese (II) ion · metal · 2 copies · chains B, E, D, F
- NA · Sodium ion · metal · chains A
- GOL · Glycerol · additive · 8 copies · chains A, C, E, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 6QTK · 2.31A structure of gepotidacin with S.aureus DNA gyrase and doubly nicked 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 B 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 6QTK · PDBe 6QTK · UniProt P66937 · UniProt Q99XG5
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