MolNFT v1 · #26064 · protein
Structural basis of mutual activation of the tryptophan synthase A2B2 complex from a hyperthermophile, pyrococcus furiosus
1WDW · Tryptophan synthase alpha chain: “Structural basis of mutual activation of the tryptophan synthase A2B2 complex from a hyperthermophile…”. X-ray diffraction, 1 ligand (PLP), 19 pockets (best druggability 0.90). MolNFT v1 #26064 on…
- PDB
- 1WDW
- Type
- protein
- Length
- 3,760 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan synthase alpha chain; Tryptophan synthase beta chain 1
- EC
- 4.2.1.20
- UniProt
- Q8U094, Q8U093
- Ligands
- PLP
- Pockets
- 19 · best druggability 0.90
Structure
x-ray diffraction · 7 distinct chains · 51% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 241 | 52% helix, 15% strand | Q8U094 |
| B, D, F, H, J, L | Tryptophan synthase beta chain 1 (EC 4.2.1.20) | protein | 385 | 48% helix, 19% strand | Q8U093 |
| C | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 241 | 52% helix, 15% strand | Q8U094 |
| E | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 248 | 50% helix, 15% strand | Q8U094 |
| G | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 242 | 52% helix, 15% strand | Q8U094 |
| I | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 244 | 51% helix, 15% strand | Q8U094 |
| K | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 234 | 52% helix, 15% strand | Q8U094 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 6 copies · chains B, D, F, H, J, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.90 | 0.92 | 141 | PLP |
| 2 | 1040 | 0.90 | 0.91 | 144 | PLP |
| 3 | 1086 | 0.87 | 0.88 | 113 | PLP |
| 4 | 628 | 0.81 | 0.86 | 66 | PLP |
| 5 | 415 | 0.77 | 0.86 | 47 | empty |
Interfaces
11 interfaces between chains.
- F–H · 1833 Ų buried · 17 hydrogen bonds · protein-protein
- J–L · 1828 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1827 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1635 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 1629 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1WDW · Structural basis of mutual activation of the tryptophan synthase a2b2 complex from a… · the same entry in another collection · chain L against L, 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 Q8U094
- Every structure of UniProt Q8U093
- Elsewhere: RCSB PDB 1WDW · PDBe 1WDW · UniProt Q8U094 · UniProt Q8U093
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