Research workbench
Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with glutamic acid linked compound 10
Analyse Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NWN
- Type
- protein
- Length
- 908 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
- L6M
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent dethiobiotin synthetase biod (EC 6.3.3.3) | protein | 227 | 43% helix, 25% strand | P9WPQ5 |
| B | ATP-dependent dethiobiotin synthetase biod (EC 6.3.3.3) | protein | 226 | 44% helix, 23% strand | P9WPQ5 |
| C | ATP-dependent dethiobiotin synthetase biod (EC 6.3.3.3) | protein | 228 | 42% helix, 24% strand | P9WPQ5 |
| D | ATP-dependent dethiobiotin synthetase biod (EC 6.3.3.3) | protein | 227 | 43% helix, 22% strand | P9WPQ5 |
Ligands and binding sites
- L6M · 5'-{[N-({(1S,2R)-2-[4-(carboxymethyl)benzene-1-carbonyl]cyclopentyl}acetyl)-L-gamma-glutamyl]amino}-2',5'-dideoxycytidine · ligand · 2 copies · chains A, B, C, D
- CIT · Citric acid · additive · 4 copies · chains A, B, 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 | 1078 | 0.79 | 0.80 | 105 | CIT |
| 2 | 241 | 0.65 | 0.83 | 44 | CIT |
| 3 | 277 | 0.64 | 0.81 | 42 | CIT, L6M |
| 4 | 300 | 0.62 | 0.80 | 55 | CIT, L6M |
| 5 | 105 | 0.39 | 0.76 | 20 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1154 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1098 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 295 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 111 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 23 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6NWN · Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with… · 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 6NWN · PDBe 6NWN · UniProt P9WPQ5
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