MolNFT v1 · #165926 · protein
Crystal structure of tryptophan synthase from M. tuberculosis - open form with BRD6309 bound
6UAP · Tryptophan synthase alpha chain: “Crystal structure of tryptophan synthase from M. tuberculosis - open form with BRD6309 bound”. X-ray diffraction, 2 ligands (MLT, H9V), 20 pockets (best druggability 0.83). MolNFT v1 #165926 on…
- PDB
- 6UAP
- Type
- protein
- Length
- 2,604 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan synthase alpha chain; Tryptophan synthase beta chain
- EC
- 4.2.1.20
- UniProt
- P9WFY1, P9WFX9
- Ligands
- MLT, H9V
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 7 distinct chains · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 249 | 51% helix, 15% strand | P9WFY1 |
| B | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 405 | 46% helix, 19% strand | P9WFX9 |
| C | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 250 | 51% helix, 15% strand | P9WFY1 |
| D | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 406 | 47% helix, 19% strand | P9WFX9 |
| E, G | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 247 | 51% helix, 15% strand | P9WFY1 |
| F | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 400 | 47% helix, 20% strand | P9WFX9 |
| H | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 400 | 49% helix, 20% strand | P9WFX9 |
Ligands and binding sites
- MLT · D-malate · ligand · 5 copies · chains B, D, F, H
- H9V · (2R,3S,4R)-3-(4'-chloro-2',6'-difluoro[1,1'-biphenyl]-4-yl)-4-(fluoromethyl)azetidine-2-carbonitrile · ligand · 4 copies · chains A, B, C, D, E, F, G, H
- FMT · Formic acid · additive · 23 copies · chains A, B, C, D, E, F, G, H
- ACT · Acetate ion · additive · 6 copies · chains D, F, C, G, H
- MLA · Malonic acid · additive · 3 copies · chains B, C, E, F
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1026 | 0.83 | 0.84 | 131 | MLT |
| 2 | 1100 | 0.83 | 0.84 | 158 | MLT |
| 3 | 162 | 0.82 | 0.97 | 28 | H9V |
| 4 | 438 | 0.82 | 0.89 | 51 | FMT |
| 5 | 397 | 0.82 | 0.90 | 52 | empty |
Interfaces
10 interfaces between chains.
- D–F · 1852 Ų buried · 22 hydrogen bonds · protein-protein
- B–H · 1828 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1368 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1367 Ų buried · 29 hydrogen bonds · protein-protein
- G–H · 1325 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 2 covalent (cofactor, covalent ligand).
Compared structures
- 6UAP · Crystal structure of tryptophan synthase from M. tuberculosis - open form with BRD6309… · the same entry in another collection · chain H against H, TM-score 1.00
- P9WFY1 · AlphaFold monomer V2.0 prediction for tryptophan synthase alpha chain (P9WFY1) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P9WFX9 · AlphaFold monomer V2.0 prediction for tryptophan synthase beta chain (P9WFX9) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 P9WFY1
- Every structure of UniProt P9WFX9
- Elsewhere: RCSB PDB 6UAP · PDBe 6UAP · UniProt P9WFY1 · UniProt P9WFX9
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