MolNFT v1 · #172147 · protein
N-terminal 47 kda fragment of the mycobacterium smegmatis DNA gyrase B subunit complexed with adpnp
6ZT3 · DNA gyrase subunit B: “N-terminal 47 kda fragment of the mycobacterium smegmatis DNA gyrase B subunit complexed with adpnp”. X-ray diffraction, 4 ligands (ANP, NA, MG), 4 pockets (best druggability 0.74). MolNFT v1 #172147 on…
- PDB
- 6ZT3
- Type
- protein
- Length
- 394 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
- A0QNE0
- Ligands
- ANP, NA, MG, K
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit B (EC 5.99.1.3) | protein | 394 | 37% helix, 24% strand | A0QNE0 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- NA · Sodium ion · metal · 3 copies · chains A
- MG · Magnesium ion · metal · chains A
- K · Potassium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A
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 | 258 | 0.74 | 0.88 | 37 | ANP, MG, K |
| 2 | 144 | 0.53 | 0.80 | 21 | EDO |
| 3 | 88 | 0.42 | 0.79 | 19 | empty |
| 4 | 58 | 0.29 | 0.74 | 11 | empty |
Compared structures
- 6ZT3 · N-terminal 47 kDa fragment of the Mycobacterium smegmatis DNA Gyrase B subunit complexed… · the same entry in another collection · chain A against A, TM-score 1.00
- A0QNE0 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (A0QNE0) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 A0QNE0
- Elsewhere: RCSB PDB 6ZT3 · PDBe 6ZT3 · UniProt A0QNE0
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