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Engineered trpb from pyrococcus furiosus, PFTRPB7E6 with (2S,3R)- ethylserine bound as the amino-acrylate
Analyse Engineered trpb from pyrococcus furiosus, PFTRPB7E6 with (2S,3R)- ethylserine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CUZ
- Type
- protein
- Length
- 1,521 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
- FEV, NA, PO4
- Pockets
- 17 · best druggability 0.82
Structure
x-ray diffraction · 4 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, 21% strand | Q8U093 |
| B | Tryptophan synthase beta chain 1 (EC 4.2.1.20) | protein | 376 | 48% helix, 19% strand | Q8U093 |
| C | Tryptophan synthase beta chain 1 (EC 4.2.1.20) | protein | 377 | 48% helix, 20% strand | Q8U093 |
| D | Tryptophan synthase beta chain 1 (EC 4.2.1.20) | protein | 385 | 49% helix, 20% strand | Q8U093 |
Ligands and binding sites
- FEV · (2E)-2-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy) methyl]pyridin-4-yl}methylidene)amino]pent-2-enoic acid · ligand · 2 copies · chains A, D
- NA · Sodium ion · metal · 6 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 165 | 0.82 | 0.98 | 34 | FEV |
| 2 | 186 | 0.82 | 0.97 | 38 | FEV |
| 3 | 524 | 0.80 | 0.86 | 74 | empty |
| 4 | 148 | 0.78 | 0.95 | 27 | empty |
| 5 | 55 | 0.71 | 0.99 | 32 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1742 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1718 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 391 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 274 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 76 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 modified (cofactor).
Compared structures
- 6CUZ · Engineered TrpB from Pyrococcus furiosus, PfTrpB7E6 with (2S,3R)-ethylserine bound as the… · the same entry in another collection · chain A 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 Q8U093
- Elsewhere: RCSB PDB 6CUZ · PDBe 6CUZ · UniProt Q8U093
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