MolNFT v1 · #161937 · protein + DNA
2.37A structure of gepotidacin with S.AUREUS DNA gyrase and uncleaved DNA
6QTP · DNA gyrase subunit B,DNA gyrase subunit B: “2.37A structure of gepotidacin with S.AUREUS DNA gyrase and uncleaved DNA”. X-ray diffraction, 4 ligands (JHN, MN, NA), 15 pockets (best druggability 0.83). MolNFT v1 #161937 on GenesisL1…
- PDB
- 6QTP
- Type
- protein + DNA
- Length
- 1,371 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
- JHN, MN, NA, SO4
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 5 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 | 44% helix, 11% strand | P66937 |
| A | DNA gyrase subunit a (EC 5.99.1.3) | protein | 473 | 49% helix, 17% strand | Q99XG5 |
| D | DNA gyrase subunit B,DNA gyrase subunit B (EC 5.99.1.3) | protein | 190 | 47% helix, 12% strand | P66937 |
| C | DNA gyrase subunit a (EC 5.99.1.3) | protein | 481 | 49% helix, 18% strand | Q99XG5 |
| E, F | DNA (5'- D(*GP*AP*GP*CP*GP*TP*AP*CP*AP*GP*CP*TP*GP*TP*AP*CP*GP*CP*TP*T)-3') | dna | 19 | — | — |
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, A, D, F
- NA · Sodium ion · metal · chains B
- SO4 · Sulfate ion · ion · chains A, C
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 955 | 0.83 | 0.84 | 96 | JHN |
| 2 | 444 | 0.71 | 0.82 | 34 | empty |
| 3 | 392 | 0.70 | 0.82 | 30 | empty |
| 4 | 627 | 0.69 | 0.78 | 72 | empty |
| 5 | 50 | 0.69 | 0.98 | 22 | empty |
Interfaces
14 interfaces between chains.
- A–C · 1618 Ų buried · 27 hydrogen bonds · protein-protein
- D–C · 1445 Ų buried · 13 hydrogen bonds · protein-protein
- B–A · 1354 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 907 Ų buried · 99 hydrogen bonds · nucleic-nucleic
- C–F · 636 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 6QTP · 2.37A structure of gepotidacin with S.aureus DNA gyrase and uncleaved 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 C 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 6QTP · PDBe 6QTP · UniProt P66937 · UniProt Q99XG5
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