MolNFT v1 · #166517 · protein
Crystal structure of tryptophan synthase from M. tuberculosis - aminoacrylate- and GSK1-bound form
6USA · Tryptophan synthase alpha chain: “Crystal structure of tryptophan synthase from M. tuberculosis - aminoacrylate- and GSK1-bound form”. X-ray diffraction, 5 ligands (PZJ, P1T, K), 20 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 6USA
- Type
- protein
- Length
- 2,602 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
- PZJ, P1T, K, NA, SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 7 distinct chains · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 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 | 404 | 46% helix, 20% strand | P9WFX9 |
| D | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 404 | 47% helix, 20% strand | P9WFX9 |
| E | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 245 | 51% helix, 15% strand | P9WFY1 |
| F | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 400 | 48% 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 | 403 | 46% helix, 19% strand | P9WFX9 |
Ligands and binding sites
- PZJ · (3R,4R)-4-[4-(2-Chlorophenyl)piperazin-1-yl]-1,1-dioxothiolan-3-ol · ligand · 4 copies · chains A, B, C, D, E, F, G, H
- P1T · 2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]acrylic acid · ligand · 4 copies · chains B, D, F, H
- K · Potassium ion · metal · 10 copies · chains B, D, F, H, G
- NA · Sodium ion · metal · 2 copies · chains H, F
- SO4 · Sulfate ion · ion · chains G, H
- FMT · Formic acid · additive · 28 copies · chains A, B, D, C, E, F, H, G
- EDO · 1,2-ethanediol · additive · 9 copies · chains B, D, F, E, G
- MLI · Malonate ion · additive · 6 copies · chains A, C, D, F, E, G
- ACT · Acetate ion · additive · 3 copies · chains D, F
- PEG · Di(hydroxyethyl)ether · additive · chains 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.84 | 0.89 | 71 | K |
| 2 | 166 | 0.82 | 0.97 | 29 | PZJ |
| 3 | 165 | 0.82 | 0.97 | 31 | PZJ |
| 4 | 155 | 0.81 | 0.97 | 27 | PZJ |
| 5 | 155 | 0.81 | 0.97 | 28 | PZJ |
Interfaces
10 interfaces between chains.
- F–H · 1739 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 1702 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1341 Ų buried · 28 hydrogen bonds · protein-protein
- G–H · 1330 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1290 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 6USA · Crystal structure of tryptophan synthase from M. tuberculosis - aminoacrylate- and… · 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 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 6USA · PDBe 6USA · UniProt P9WFY1 · UniProt P9WFX9
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