MolNFT v1 · #24876 · protein
X-ray crystal structure of the tryptophan synthase B2 subunit from hyperthermophile, pyrococcus furiosus
1V8Z · Tryptophan synthase beta chain 1: “X-ray crystal structure of the tryptophan synthase B2 subunit from hyperthermophile, pyrococcus furiosus”. X-ray diffraction, 2 ligands (PLP, NA), 16 pockets (best druggability 0.90). MolNFT v1…
- PDB
- 1V8Z
- Type
- protein
- Length
- 1,545 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
- PLP, NA
- Pockets
- 16 · best druggability 0.90
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan synthase beta chain 1 (EC 4.2.1.20) | protein | 386 | 48% helix, 21% strand | Q8U093 |
| B, C | Tryptophan synthase beta chain 1 (EC 4.2.1.20) | protein | 387 | 48% helix, 20% strand | Q8U093 |
| D | Tryptophan synthase beta chain 1 (EC 4.2.1.20) | protein | 385 | 47% helix, 21% strand | Q8U093 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.90 | 0.96 | 107 | PLP |
| 2 | 389 | 0.87 | 0.96 | 81 | PLP |
| 3 | 153 | 0.80 | 0.97 | 36 | PLP |
| 4 | 609 | 0.71 | 0.79 | 70 | empty |
| 5 | 659 | 0.67 | 0.76 | 87 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1875 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1868 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 252 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 129 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 89 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1V8Z · X-ray crystal structure of the Tryptophan Synthase b2 Subunit from Hyperthermophile… · the same entry in another collection · chain A against A, 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 B 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 1V8Z · PDBe 1V8Z · UniProt Q8U093
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