MolNFT v1 · #23818 · protein
Tryptophan synthase (E.C.4.2.1.20) with a mutation of lys 87->thr in the B subunit and in the presence of ligand L-serine
1UBS: “Tryptophan synthase (E.C.4.2.1.20) with a mutation of lys 87->thr in the B subunit and in the presence of…”. X-ray diffraction, 3 ligands (SER, PLP, NA), 7 pockets (best druggability 0.82). MolNFT v1 #23818 on GenesisL1: 3D…
- PDB
- 1UBS
- Type
- protein
- Length
- 646 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tryptophan synthase
- EC
- 4.2.1.20
- UniProt
- P00929, P00933
- Ligands
- SER, PLP, NA
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan synthase (EC 4.2.1.20) | protein | 257 | 53% helix, 14% strand | P00929 |
| B | Tryptophan synthase (EC 4.2.1.20) | protein | 389 | 46% helix, 22% strand | P00933 |
Ligands and binding sites
- SER · Serine · ligand · chains B
- 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
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 183 | 0.82 | 0.97 | 35 | SER, PLP |
| 2 | 361 | 0.71 | 0.83 | 51 | empty |
| 3 | 156 | 0.50 | 0.79 | 32 | empty |
| 4 | 82 | 0.46 | 0.81 | 15 | empty |
| 5 | 74 | 0.37 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1368 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 1UBS · Tryptophan synthase (E.C.4.2.1.20) with a mutation of lys 87->thr in the B subunit and in… · the same entry in another collection · chain A against A, TM-score 1.00
- P00929 · AlphaFold monomer V2.0 prediction for tryptophan synthase alpha chain (P00929) · a predicted model of the same protein · chain A 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 P00929
- Every structure of UniProt P00933
- Elsewhere: RCSB PDB 1UBS · PDBe 1UBS · UniProt P00929 · UniProt P00933
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