MolNFT v1 · #80620 · protein
S. aureus gyrb ATPase domain in complex with small molecule inhibitor
3U2D · DNA gyrase subunit B: “S. aureus gyrb ATPase domain in complex with small molecule inhibitor”. X-ray diffraction, 2 ligands (08B, MG), 4 pockets (best druggability 0.52). MolNFT v1 #80620 on GenesisL1: 3D structure, binding sites…
- PDB
- 3U2D
- Type
- protein
- Length
- 380 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
- 08B, MG
- Pockets
- 4 · best druggability 0.52
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 | 194 | 35% helix, 30% strand | P0A0K8 |
| B | DNA gyrase subunit B (EC 5.99.1.3) | protein | 186 | 33% helix, 32% strand | P0A0K8 |
Ligands and binding sites
- 08B · 4-bromo-5-methyl-N-[1-(3-nitropyridin-2-yl)piperidin-4-yl]-1H-pyrrole-2-carboxamide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.52 | 0.80 | 23 | 08B, MG |
| 2 | 139 | 0.50 | 0.79 | 23 | 08B |
| 3 | 160 | 0.46 | 0.76 | 19 | empty |
| 4 | 56 | 0.28 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 285 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3U2D · S. aureus GyrB ATPase domain in complex with small molecule inhibitor · 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 3U2D · PDBe 3U2D · UniProt P0A0K8
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