Research workbench
Crystal structure of mycobacterium tuberculosis dethiobiotin synthetase in complex with fragment degradation product B9D
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
- 6NLZ
- Type
- protein
- Length
- 909 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
- KSJ, KSP, SO4
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent dethiobiotin synthetase biod (EC 6.3.3.3) | protein | 227 | 44% helix, 24% strand | P9WPQ5 |
| B | ATP-dependent dethiobiotin synthetase biod (EC 6.3.3.3) | protein | 226 | 43% helix, 23% strand | P9WPQ5 |
| C | ATP-dependent dethiobiotin synthetase biod (EC 6.3.3.3) | protein | 229 | 41% 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
- KSJ · [(1S,2R)-2-(2-hydroxybenzene-1-carbonyl) cyclopentyl]acetic acid · ligand · 4 copies · chains A, B, C, D
- KSP · [(1R,2S)-2-(2-hydroxybenzene-1-carbonyl) cyclopentyl]acetic acid · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 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 | 988 | 0.79 | 0.81 | 98 | SO4, KSJ, KSP |
| 2 | 322 | 0.67 | 0.82 | 52 | KSJ, KSP, SO4 |
| 3 | 304 | 0.66 | 0.82 | 48 | SO4, KSJ, KSP |
| 4 | 272 | 0.66 | 0.82 | 47 | KSJ, KSP, SO4 |
| 5 | 130 | 0.41 | 0.75 | 21 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1113 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1062 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 230 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 117 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6NLZ · 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 6NLZ · PDBe 6NLZ · UniProt P9WPQ5
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