MolNFT v1 · #180497 · protein
Mycobacterium tuberculosis dethiobiotin synthetase in complex with tetrazole 1
7L1J · ATP-dependent dethiobiotin synthetase biod: “Mycobacterium tuberculosis dethiobiotin synthetase in complex with tetrazole 1”. X-ray diffraction, 2 ligands (XES, SO4), 6 pockets (best druggability 0.81). MolNFT v1 #180497 on…
- PDB
- 7L1J
- 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
- XES, SO4
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 3 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 | 44% helix, 24% strand | P9WPQ5 |
| B, D | 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 | 43% helix, 24% strand | P9WPQ5 |
Ligands and binding sites
- XES · {(1R,2R)-2-[4-(1H-tetrazol-5-yl)benzene-1-carbonyl]cyclopentyl}propanedioic acid · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
- GOL · Glycerol · 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 | 1044 | 0.81 | 0.82 | 108 | XES, SO4 |
| 2 | 440 | 0.69 | 0.80 | 61 | XES, SO4 |
| 3 | 319 | 0.65 | 0.81 | 58 | XES, SO4 |
| 4 | 306 | 0.64 | 0.80 | 54 | XES, SO4 |
| 5 | 124 | 0.42 | 0.76 | 21 | GOL |
Interfaces
5 interfaces between chains.
- A–B · 1101 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1092 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 342 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 118 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 50 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7L1J · Mycobacterium tuberculosis dethiobiotin synthetase in complex with Tetrazole 1 · 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 7L1J · PDBe 7L1J · UniProt P9WPQ5
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