MolNFT v1 · #50404 · protein
Tryptophan synthase complexed with igp, internal aldimine, pH 9.0
2RH9 · Tryptophan synthase alpha chain: “Tryptophan synthase complexed with igp, internal aldimine, pH 9.0”. X-ray diffraction, 3 ligands (IGP, PLP, NA), 5 pockets (best druggability 0.76). MolNFT v1 #50404 on GenesisL1: 3D structure…
- PDB
- 2RH9
- Type
- protein
- Length
- 648 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan synthase alpha chain; Tryptophan synthase beta chain
- EC
- 4.2.1.20
- UniProt
- P00929, P0A2K1
- Ligands
- IGP, PLP, NA
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 254 | 52% helix, 15% strand | P00929 |
| B | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 394 | 48% helix, 22% strand | P0A2K1 |
Ligands and binding sites
- IGP · Indole-3-glycerol phosphate · ligand · chains A
- PLP · Pyridoxal-5'-phosphate · ligand · chains B
- NA · Sodium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 345 | 0.76 | 0.87 | 60 | PLP |
| 2 | 323 | 0.67 | 0.81 | 33 | IGP |
| 3 | 94 | 0.42 | 0.77 | 15 | empty |
| 4 | 64 | 0.38 | 0.79 | 19 | empty |
| 5 | 80 | 0.36 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1353 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 2RH9 · Tryptophan synthase complexed with IGP, internal aldimine, pH 9.0 · 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 P00929
- Every structure of UniProt P0A2K1
- Elsewhere: RCSB PDB 2RH9 · PDBe 2RH9 · UniProt P00929 · UniProt P0A2K1
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