MolNFT v1 · #125254 · protein
Escherichia COLI DNA gyrase B in complex with benzothiazole-based inhibitor
5L3J · DNA gyrase subunit B: “Escherichia COLI DNA gyrase B in complex with benzothiazole-based inhibitor”. X-ray diffraction, 2 ligands (6G9, IOD), 2 pockets (best druggability 0.60). MolNFT v1 #125254 on GenesisL1: 3D structure, binding…
- PDB
- 5L3J
- Type
- protein
- Length
- 360 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit B
- EC
- 5.99.1.3
- UniProt
- P0AES6
- Ligands
- 6G9, IOD
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit B (EC 5.99.1.3) | protein | 360 | 39% helix, 27% strand | P0AES6 |
Ligands and binding sites
- 6G9 · 2-[[2-[[4,5-bis(bromanyl)-1~{H}-pyrrol-2-yl]carbonylamino]-1,3-benzothiazol-6-yl]amino]-2-oxidanylidene-ethanoic acid · ligand · chains A
- IOD · Iodide ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.60 | 0.76 | 47 | empty |
| 2 | 110 | 0.51 | 0.81 | 15 | 6G9 |
Compared structures
- 5L3J · Escherichia COLI DNA gyrase B in complex with benzothiazole-based inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P0AES6 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (P0AES6) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P0AES6
- Elsewhere: RCSB PDB 5L3J · PDBe 5L3J · UniProt P0AES6
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