MolNFT v1 · #134690 · protein
Crystal structure of tryptophan synthase from M. tuberculosis - aminoacrylate-bound form
5TCG · Tryptophan synthase alpha chain: “Crystal structure of tryptophan synthase from M. tuberculosis - aminoacrylate-bound form”. X-ray diffraction, 2 ligands (P1T, CS), 20 pockets (best druggability 0.83). MolNFT v1 #134690 on…
- PDB
- 5TCG
- Type
- protein
- Length
- 2,587 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, CS
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 249 | 52% helix, 15% strand | P9WFY1 |
| B, H, F, D | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 399 | 47% helix, 20% strand | P9WFX9 |
| G | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 248 | 53% helix, 15% strand | P9WFY1 |
| E | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 245 | 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
- CS · Cesium ion · metal · 9 copies · chains B, H, F, D
- FMT · Formic acid · additive · 25 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 665 | 0.83 | 0.87 | 79 | FMT |
| 2 | 109 | 0.79 | 0.99 | 33 | P1T |
| 3 | 107 | 0.79 | 0.98 | 32 | P1T |
| 4 | 110 | 0.78 | 0.98 | 32 | P1T |
| 5 | 124 | 0.78 | 0.96 | 23 | empty |
Interfaces
10 interfaces between chains.
- H–F · 1744 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 1713 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1317 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1304 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 1296 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5TCG · Crystal structure of tryptophan synthase from M. tuberculosis - aminoacrylate-bound form · the same entry in another collection · chain A against A, TM-score 1.00
- P9WFY1 · AlphaFold monomer V2.0 prediction for tryptophan synthase alpha chain (P9WFY1) · a predicted model of the same protein · chain E 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 5TCG · PDBe 5TCG · UniProt P9WFY1 · UniProt P9WFX9
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