MolNFT v1 · #109163 · protein
N-terminal 43 kda fragment of the E. COLI DNA gyrase B subunit grown from no salt condition
4WUD · DNA gyrase subunit B: “N-terminal 43 kda fragment of the E. COLI DNA gyrase B subunit grown from no salt condition”. X-ray diffraction, 4 ligands (ANP, MG, NA), 2 pockets (best druggability 0.73). MolNFT v1 #109163 on GenesisL1: 3D…
- PDB
- 4WUD
- Type
- protein
- Length
- 384 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
- ANP, MG, NA, CL
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit B (EC 5.99.1.3) | protein | 384 | 36% helix, 24% strand | P0AES6 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- MG · Magnesium ion · metal · chains A
- NA · Sodium ion · metal · chains A
- CL · Chloride 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 | 258 | 0.73 | 0.87 | 43 | ANP, MG |
| 2 | 233 | 0.51 | 0.76 | 32 | empty |
Compared structures
- 4WUD · N-terminal 43 kDa fragment of the E. coli DNA gyrase B subunit grown from no salt… · 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 0.96
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 P0AES6
- Elsewhere: RCSB PDB 4WUD · PDBe 4WUD · UniProt P0AES6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.