Research workbench
Crystal structure of tryptophan synthase from M. tuberculosis - ligand-free form
Analyse Crystal structure of tryptophan synthase from M. tuberculosis - ligand-free form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TCF
- Type
- protein
- Length
- 2,596 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
- K
- Pockets
- 19 · best druggability 0.88
Structure
x-ray diffraction · 8 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 | 53% helix, 16% strand | P9WFY1 |
| B | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 405 | 46% helix, 19% strand | P9WFX9 |
| G | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 247 | 52% helix, 15% strand | P9WFY1 |
| H | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 405 | 46% helix, 19% strand | P9WFX9 |
| E | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 245 | 52% helix, 15% strand | P9WFY1 |
| F | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 399 | 46% helix, 20% strand | P9WFX9 |
| C | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 248 | 52% helix, 15% strand | P9WFY1 |
| D | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 398 | 47% helix, 20% strand | P9WFX9 |
Ligands and binding sites
- K · Potassium ion · metal · 3 copies · chains B, D, H
- FMT · Formic acid · additive · 21 copies · chains A, B, G, H, E, F, C, D
- 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
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1111 | 0.88 | 0.90 | 139 | K |
| 2 | 878 | 0.85 | 0.87 | 119 | FMT |
| 3 | 1069 | 0.84 | 0.85 | 121 | empty |
| 4 | 523 | 0.80 | 0.86 | 67 | MLI, FMT |
| 5 | 364 | 0.78 | 0.88 | 56 | MLI, FMT |
Interfaces
10 interfaces between chains.
- B–D · 1843 Ų buried · 26 hydrogen bonds · protein-protein
- H–F · 1834 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1392 Ų buried · 25 hydrogen bonds · protein-protein
- G–H · 1371 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1332 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 5TCF · Crystal structure of tryptophan synthase from M. tuberculosis - ligand-free form · 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 G 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 5TCF · PDBe 5TCF · UniProt P9WFY1 · UniProt P9WFX9
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