Research workbench
Crystal structure of tryptophan synthase from M. tuberculosis - aminoacrylate- and BRD0059-bound form
Analyse Crystal structure of tryptophan synthase from M. tuberculosis - aminoacrylate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DWE
- Type
- protein
- Length
- 2,597 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
- P1T, HDJ, CS
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 7 distinct chains · 49% 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, 16% strand | P9WFY1 |
| B | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 404 | 47% helix, 21% strand | P9WFX9 |
| G | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 248 | 51% helix, 15% strand | P9WFY1 |
| H | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 404 | 46% helix, 21% strand | P9WFX9 |
| E | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 246 | 50% helix, 15% strand | P9WFY1 |
| F, D | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 399 | 48% helix, 20% strand | P9WFX9 |
| C | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 248 | 51% helix, 15% strand | P9WFY1 |
Ligands and binding sites
- P1T · 2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]acrylic acid · ligand · 4 copies · chains B, H, F, D
- HDJ · (2R,3S,4R)-3-(2',6'-difluoro-4'-methyl[1,1'-biphenyl]-4-yl)-4-(fluoromethyl)azetidine-2-carbonitrile · ligand · 4 copies · chains A, B, G, H, E, F, C, D
- CS · Cesium ion · metal · 9 copies · chains B, H, D, F
- FMT · Formic acid · additive · 33 copies · chains A, B, D, F, G, H, E, C
- MLI · Malonate ion · additive · 4 copies · chains A, G, E, C
- ACT · Acetate ion · additive · 3 copies · chains A, B, G, H
- MLA · Malonic acid · additive · 2 copies · chains H, F, D
- EDO · 1,2-ethanediol · additive · chains B, H, F
- PGE · Triethylene glycol · additive · chains 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 161 | 0.82 | 0.97 | 28 | HDJ |
| 2 | 410 | 0.82 | 0.90 | 52 | FMT |
| 3 | 146 | 0.81 | 0.97 | 30 | HDJ |
| 4 | 123 | 0.81 | 0.99 | 33 | P1T |
| 5 | 140 | 0.81 | 0.97 | 27 | HDJ, ACT |
Interfaces
10 interfaces between chains.
- H–F · 1742 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1732 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1379 Ų buried · 30 hydrogen bonds · protein-protein
- G–H · 1346 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1306 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 6DWE · Crystal structure of tryptophan synthase from M. tuberculosis - aminoacrylate- and… · the same entry in another collection · chain D against D, 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
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 6DWE · PDBe 6DWE · UniProt P9WFY1 · UniProt P9WFX9
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