Research workbench
Trpb from pyrococcus furiosus with L-serine bound as the external aldimine
Analyse Trpb from pyrococcus furiosus with L-serine bound as the external aldimine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DW0
- Type
- protein
- Length
- 1,543 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
- PLS, NA
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 2 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 | 388 | 48% helix, 20% strand | Q8U093 |
| B, C, D | Tryptophan synthase beta chain 1 (EC 4.2.1.20) | protein | 385 | 49% helix, 20% strand | Q8U093 |
Ligands and binding sites
- PLS · [3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl]-serine · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 161 | 0.82 | 0.98 | 39 | PLS |
| 2 | 155 | 0.81 | 0.97 | 38 | PLS |
| 3 | 149 | 0.81 | 0.97 | 34 | PLS |
| 4 | 149 | 0.80 | 0.97 | 34 | PLS |
| 5 | 1073 | 0.80 | 0.81 | 121 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1865 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1787 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 228 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 154 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 67 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5DW0 · TrpB from Pyrococcus furiosus with L-serine bound as the external aldimine · the same entry in another collection · chain D against D, 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 A 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 5DW0 · PDBe 5DW0 · UniProt Q8U093
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