Research workbench
X-ray crystal structure of tryptophan synthase complex from pyrococcus furiosus at 2.76 a
Analyse X-ray crystal structure of tryptophan synthase complex from pyrococcus furiosus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E0K
- Type
- protein
- Length
- 3,757 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan synthase alpha chain; Tryptophan synthase beta chain 1
- EC
- 4.2.1.20
- UniProt
- Q8U094, Q8U093
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, I | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 242 | 52% helix, 17% strand | Q8U094 |
| B, D, F, H, J, L | Tryptophan synthase beta chain 1 (EC 4.2.1.20) | protein | 385 | 47% helix, 20% strand | Q8U093 |
| C, G | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 241 | 49% helix, 16% strand | Q8U094 |
| E | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 241 | 51% helix, 17% strand | Q8U094 |
| K | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 240 | 49% helix, 17% strand | Q8U094 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 6 copies · chains B, D, F, H, J, L
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 | 1004 | 0.85 | 0.86 | 108 | PO4 |
| 2 | 1059 | 0.83 | 0.84 | 119 | PO4 |
| 3 | 477 | 0.81 | 0.89 | 65 | empty |
| 4 | 467 | 0.80 | 0.88 | 65 | empty |
| 5 | 546 | 0.80 | 0.86 | 66 | PO4 |
Interfaces
17 interfaces between chains.
- J–L · 1855 Ų buried · 16 hydrogen bonds · protein-protein
- F–H · 1836 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1828 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1704 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 1702 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (cofactor).
Compared structures
- 5E0K · X-ray crystal structure of tryptophan synthase complex from Pyrococcus furiosus at 2.76 A · the same entry in another collection · chain L against L, 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 Q8U094
- Every structure of UniProt Q8U093
- Elsewhere: RCSB PDB 5E0K · PDBe 5E0K · UniProt Q8U094 · UniProt Q8U093
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