Research workbench
Crystal structure of tryptophan synthase from M. tuberculosis - aminoacrylate- and GSK2-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
- 6U6C
- Type
- protein
- Length
- 2,609 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
- PZV, P1T, ALA, K, NA
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G | 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 | 405 | 47% helix, 20% strand | P9WFX9 |
| D, F, H | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 404 | 48% helix, 21% strand | P9WFX9 |
| E | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 245 | 51% helix, 15% strand | P9WFY1 |
Ligands and binding sites
- PZV · 1-(2-fluorobenzene-1-carbonyl)-N-methyl-2,3-dihydro-1H-indole-5-sulfonamide · 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
- ALA · Alanine · ligand · chains E
- K · Potassium ion · metal · 8 copies · chains B, C, D, F, G, H
- NA · Sodium ion · metal · chains B, F, H
- FMT · Formic acid · additive · 92 copies · chains A, B, D, F, H, C, E, G
- EDO · 1,2-ethanediol · additive · 24 copies · chains A, B, D, C, E, F, H, G
- MLI · Malonate ion · additive · 6 copies · chains A, C, E, D, F, G, H
- ACT · Acetate ion · additive · 5 copies · chains A, B, F, G, H
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains B, F, H, G
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains B, D, F, H
- PGE · Triethylene glycol · additive · 2 copies · chains D, F
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 | 156 | 0.82 | 0.97 | 30 | PZV |
| 2 | 487 | 0.82 | 0.89 | 53 | FMT, EPE, K |
| 3 | 150 | 0.81 | 0.97 | 29 | PZV |
| 4 | 154 | 0.81 | 0.96 | 27 | PZV |
| 5 | 151 | 0.81 | 0.96 | 30 | PZV |
Interfaces
10 interfaces between chains.
- F–H · 1750 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 1734 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1341 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 1298 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 1296 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 6U6C · 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 6U6C · PDBe 6U6C · UniProt P9WFY1 · UniProt P9WFX9
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