MolNFT v1 · #158112 · protein
Crystal structure of dethiobiotin synthetase from mycobacterium tuberculosis in complex with 2'-deoxycytidine diphosphate
6NKB · ATP-dependent dethiobiotin synthetase biod: “Crystal structure of dethiobiotin synthetase from mycobacterium tuberculosis in complex with 2'-deoxycytidine…”. X-ray diffraction, 2 ligands (YYY, MG), 6 pockets (best druggability…
- PDB
- 6NKB
- Type
- protein
- Length
- 907 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-dependent dethiobiotin synthetase biod
- EC
- 6.3.3.3
- UniProt
- P9WPQ5
- Ligands
- YYY, MG
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent dethiobiotin synthetase biod (EC 6.3.3.3) | protein | 227 | 42% helix, 25% strand | P9WPQ5 |
| B | ATP-dependent dethiobiotin synthetase biod (EC 6.3.3.3) | protein | 226 | 42% helix, 23% strand | P9WPQ5 |
| C, D | ATP-dependent dethiobiotin synthetase biod (EC 6.3.3.3) | protein | 227 | 42% helix, 24% strand | P9WPQ5 |
Ligands and binding sites
- YYY · Deoxycytidine diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1069 | 0.79 | 0.81 | 101 | empty |
| 2 | 260 | 0.65 | 0.82 | 51 | YYY, MG |
| 3 | 279 | 0.62 | 0.80 | 49 | MG |
| 4 | 258 | 0.59 | 0.79 | 44 | YYY, MG |
| 5 | 104 | 0.37 | 0.75 | 20 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1171 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1044 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 358 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 103 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 30 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6NKB · Crystal structure of Dethiobiotin Synthetase from Mycobacterium tuberculosis in complex… · the same entry in another collection · chain D against D, TM-score 1.00
- P9WPQ5 · AlphaFold monomer V2.0 prediction for dethiobiotin synthetase biod (P9WPQ5) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P9WPQ5
- Elsewhere: RCSB PDB 6NKB · PDBe 6NKB · UniProt P9WPQ5
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