MolNFT v1 · #176497 · protein
E. COLI gyrb ATPase domain in complex with 4-nitropheno
7DOR · DNA gyrase subunit B: “E. COLI gyrb ATPase domain in complex with 4-nitropheno”. X-ray diffraction, 3 ligands (NPO, AX7, PO4), 4 pockets (best druggability 0.63). MolNFT v1 #176497 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7DOR
- Type
- protein
- Length
- 373 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit B
- EC
- 5.6.2.2
- UniProt
- A0A4S5B230
- Ligands
- NPO, AX7, PO4
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit B (EC 5.6.2.2) | protein | 185 | 30% helix, 30% strand | A0A4S5B230 |
| B | DNA gyrase subunit B (EC 5.6.2.2) | protein | 188 | 29% helix, 30% strand | A0A4S5B230 |
Ligands and binding sites
- NPO · P-nitrophenol · ligand · 2 copies · chains A, B
- AX7 · 1H-benzimidazol-2-amine · ligand · chains A, B
- PO4 · Phosphate ion · ion · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 226 | 0.63 | 0.83 | 28 | AX7 |
| 2 | 65 | 0.61 | 0.91 | 19 | NPO |
| 3 | 71 | 0.57 | 0.88 | 16 | NPO |
| 4 | 59 | 0.30 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 462 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7DOR · E. coli GyrB ATPase domain in complex with 4-nitropheno · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A4S5B230
- Elsewhere: RCSB PDB 7DOR · PDBe 7DOR · UniProt A0A4S5B230
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