MolNFT v1 · #115782 · protein
Crystal structure of the ATP binding domain of S. aureus gyrb complexed with a fragment
5CTW · DNA gyrase subunit B: “Crystal structure of the ATP binding domain of S. aureus gyrb complexed with a fragment”. X-ray diffraction, 3 ligands (55D, MG, CL), 2 pockets (best druggability 0.47). MolNFT v1 #115782 on GenesisL1: 3D…
- PDB
- 5CTW
- Type
- protein
- Length
- 384 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
- 55D, MG, CL
- Pockets
- 2 · best druggability 0.47
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 | 34% helix, 31% strand | P0A0K8 |
| B | DNA gyrase subunit B (EC 5.99.1.3) | protein | 192 | 33% helix, 31% strand | P0A0K8 |
Ligands and binding sites
- 55D · 2-(butanoylamino)thiophene-3-carboxamide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 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 | 109 | 0.47 | 0.80 | 22 | 55D |
| 2 | 108 | 0.46 | 0.79 | 23 | 55D |
Interfaces
1 interface between chains.
- A–B · 256 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5CTW · Crystal structure of the ATP binding domain of S. aureus GyrB complexed with a fragment · 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 0.96
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 5CTW · PDBe 5CTW · UniProt P0A0K8
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