Research workbench
2.31A structure of gepotidacin with S.AUREUS DNA gyrase and doubly nicked DNA
Analyse 2.31A structure of gepotidacin with S.AUREUS DNA gyrase and doubly nicked DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QTK
- Type
- protein + DNA
- Length
- 1,390 residues
- Chains
- 6
- 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
- JHN, MN, NA
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | DNA gyrase subunit B (EC 5.99.1.3) | protein | 192 | 48% helix, 11% strand | P66937 |
| A | DNA gyrase subunit a (EC 5.99.1.3) | protein | 484 | 48% helix, 18% strand | Q99XG5 |
| C | DNA gyrase subunit a (EC 5.99.1.3) | protein | 482 | 49% helix, 18% strand | Q99XG5 |
| E, F | DNA (5'- D(*AP*GP*CP*CP*GP*TP*AP*G*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3') | 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.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 256 | 0.76 | 0.89 | 44 | GOL |
| 2 | 491 | 0.75 | 0.84 | 51 | GOL, JHN |
| 3 | 455 | 0.74 | 0.84 | 32 | empty |
| 4 | 276 | 0.74 | 0.87 | 46 | empty |
| 5 | 447 | 0.71 | 0.82 | 33 | empty |
Interfaces
14 interfaces between chains.
- A–C · 1680 Ų buried · 23 hydrogen bonds · protein-protein
- B–A · 1669 Ų buried · 16 hydrogen bonds · protein-protein
- D–C · 1522 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 898 Ų buried · 80 hydrogen bonds · nucleic-nucleic
- A–D · 713 Ų buried · 7 hydrogen bonds · protein-protein
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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