MolNFT v1 · #117031 · protein
Tryptophan synthase beta-subunit from pyrococcus furiosus with product L-tryptophan non-covalently bound in the active site
5DW3 · Tryptophan synthase beta chain 1: “Tryptophan synthase beta-subunit from pyrococcus furiosus with product L-tryptophan non-covalently bound in…”. X-ray diffraction, 3 ligands (TRP, NA, PO4), 16 pockets (best druggability 0.83).…
- PDB
- 5DW3
- Type
- protein
- Length
- 1,537 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan synthase beta chain 1
- EC
- 4.2.1.20
- UniProt
- Q8U093
- Ligands
- TRP, NA, PO4
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan synthase beta chain 1 (EC 4.2.1.20) | protein | 383 | 49% helix, 20% strand | Q8U093 |
| B | Tryptophan synthase beta chain 1 (EC 4.2.1.20) | protein | 386 | 49% helix, 20% strand | Q8U093 |
| C, D | Tryptophan synthase beta chain 1 (EC 4.2.1.20) | protein | 384 | 49% helix, 20% strand | Q8U093 |
Ligands and binding sites
- TRP · Tryptophan · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 198 | 0.83 | 0.98 | 50 | empty |
| 2 | 210 | 0.83 | 0.96 | 44 | empty |
| 3 | 1144 | 0.81 | 0.82 | 107 | empty |
| 4 | 87 | 0.76 | 0.98 | 19 | TRP |
| 5 | 80 | 0.74 | 0.97 | 21 | TRP |
Interfaces
5 interfaces between chains.
- A–B · 1808 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1758 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 310 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 289 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 84 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 5DW3 · Tryptophan Synthase beta-subunit from Pyrococcus furiosus with product L-tryptophan… · the same entry in another collection · chain C against C, TM-score 1.00
- Q8U093 · AlphaFold monomer V2.0 prediction for tryptophan synthase beta chain 1 (Q8U093) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 Q8U093
- Elsewhere: RCSB PDB 5DW3 · PDBe 5DW3 · UniProt Q8U093
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