Research workbench
Crystal structure of tryptophan synthase from M. tuberculosis - aminoacrylate and BRD4592-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
- 5TCJ
- Type
- protein
- Length
- 2,589 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, 79V, CS
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 50% 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, F, D | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 399 | 48% helix, 21% strand | P9WFX9 |
| G | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 248 | 52% helix, 15% strand | P9WFY1 |
| H | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 401 | 47% helix, 21% strand | P9WFX9 |
| E | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 246 | 53% helix, 15% strand | P9WFY1 |
| C | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 248 | 52% 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
- 79V · (2R,3S,4R)-3-(2'-fluoro[1,1'-biphenyl]-4-yl)-4-(hydroxymethyl)azetidine-2-carbonitrile · ligand · 4 copies · chains A, B, G, H, E, F, C, D
- CS · Cesium ion · metal · 9 copies · chains B, D, H, F
- FMT · Formic acid · additive · 22 copies · chains A, B, D, G, H, F, E, C
- MLI · Malonate ion · additive · 4 copies · chains A, G, E, C
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 | 1031 | 0.85 | 0.86 | 100 | FMT |
| 2 | 141 | 0.81 | 0.97 | 26 | 79V |
| 3 | 131 | 0.81 | 0.97 | 27 | 79V |
| 4 | 118 | 0.80 | 0.99 | 33 | P1T |
| 5 | 137 | 0.79 | 0.96 | 28 | 79V |
Interfaces
10 interfaces between chains.
- H–F · 1752 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 1721 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1379 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 1364 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1322 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5TCJ · 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 5TCJ · PDBe 5TCJ · UniProt P9WFY1 · UniProt P9WFX9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.