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Engineered tryptophan synthase b-subunit from Pyrococcus furiosus, PfTrpB2B9-H275E with L-Trp non-covalently bound
Analyse Engineered tryptophan synthase b-subunit 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
- 7ROF
- Type
- protein
- Length
- 1,536 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.39
- Source
- Pyrococcus furiosus
- Molecule
- Tryptophan synthase beta chain 1
- EC
- 4.2.1.20
- UniProt
- Q8U093
- Ligands
- TRP, NA
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · resolution 2.39 · 2 distinct chains · 49% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Tryptophan synthase beta chain 1 (EC 4.2.1.20) | protein | 385 | 49% helix, 20% strand | Q8U093 |
| C | Tryptophan synthase beta chain 1 (EC 4.2.1.20) | protein | 381 | 49% helix, 19% strand | Q8U093 |
Ligands and binding sites
- TRP · Tryptophan · ligand · 2 copies · chains A, 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
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1181 | 0.85 | 0.85 | 135 | TRP |
| 2 | 447 | 0.76 | 0.85 | 65 | empty |
| 3 | 387 | 0.74 | 0.84 | 46 | empty |
| 4 | 325 | 0.71 | 0.84 | 42 | TRP |
| 5 | 510 | 0.62 | 0.75 | 51 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1712 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1610 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 76 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 7ROF · Engineered tryptophan synthase B-subunit from pyrococcus furiosus, PFTRPB2B9-H275E with… · 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 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 7ROF · PDBe 7ROF · UniProt Q8U093
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