MolNFT v1 · #116210 · protein
Crystal structure of the ATP binding domain of S. aureus gyrb complexed with a ligand
5D6Q · DNA gyrase subunit B: “Crystal structure of the ATP binding domain of S. aureus gyrb complexed with a ligand”. X-ray diffraction, 2 ligands (57V, MG), 2 pockets (best druggability 0.50). MolNFT v1 #116210 on GenesisL1: 3D structure…
- PDB
- 5D6Q
- Type
- protein
- Length
- 378 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit B
- EC
- 5.99.1.3
- UniProt
- P0A0K8
- Ligands
- 57V, MG
- Pockets
- 2 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit B (EC 5.99.1.3) | protein | 192 | 35% helix, 31% strand | P0A0K8 |
| B | DNA gyrase subunit B (EC 5.99.1.3) | protein | 186 | 33% helix, 32% strand | P0A0K8 |
Ligands and binding sites
- 57V · 1-ethyl-3-{4-[(E)-2-(pyridin-3-yl)ethenyl]-5-(1H-pyrrol-2-yl)-1,3-thiazol-2-yl}urea · ligand · chains B
- MG · Magnesium ion · metal · 2 copies · chains B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.50 | 0.79 | 21 | empty |
| 2 | 123 | 0.45 | 0.78 | 21 | 57V |
Interfaces
1 interface between chains.
- A–B · 240 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5D6Q · Crystal structure of the ATP binding domain of S. aureus GyrB complexed with a ligand · the same entry in another collection · chain A against A, TM-score 1.00
- P0A0K8 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (P0A0K8) · 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 P0A0K8
- Elsewhere: RCSB PDB 5D6Q · PDBe 5D6Q · UniProt P0A0K8
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