MolNFT v1 · #149799 · protein
Extremely 'open' clamp structure of DNA gyrase: role of the corynebacteriales gyrb specific insert
6GAU · DNA gyrase subunit B,DNA gyrase subunit a: “Extremely 'open' clamp structure of DNA gyrase: role of the corynebacteriales gyrb specific insert”. X-ray diffraction, 2 ligands (ANP, MG), 20 pockets (best druggability 0.79). MolNFT v1…
- PDB
- 6GAU
- Type
- protein
- Length
- 2,156 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit B,DNA gyrase subunit a
- EC
- 5.99.1.3
- UniProt
- F6N7X0, P9WG47
- Ligands
- ANP, MG
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit B,DNA gyrase subunit a (EC 5.99.1.3) | protein | 1088 | 43% helix, 19% strand | F6N7X0, P9WG47 |
| B | DNA gyrase subunit B,DNA gyrase subunit a (EC 5.99.1.3) | protein | 1068 | 43% helix, 19% strand | F6N7X0, P9WG47 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 846 | 0.79 | 0.82 | 73 | empty |
| 2 | 731 | 0.78 | 0.82 | 71 | empty |
| 3 | 378 | 0.72 | 0.83 | 44 | empty |
| 4 | 757 | 0.68 | 0.76 | 74 | empty |
| 5 | 353 | 0.68 | 0.81 | 42 | empty |
Interfaces
1 interface between chains.
- A–B · 4917 Ų buried · 94 hydrogen bonds · protein-protein
Compared structures
- 6GAU · Extremely 'open' clamp structure of DNA gyrase: role of the Corynebacteriales GyrB… · the same entry in another collection · chain A against A, TM-score 1.00
- P9WG47 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit a (P9WG47) · a predicted model of the same protein · chain B against A, TM-score 0.44
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 F6N7X0
- Every structure of UniProt P9WG47
- Elsewhere: RCSB PDB 6GAU · PDBe 6GAU · UniProt F6N7X0 · UniProt P9WG47
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