MolNFT v1 · #167259 · protein
Tryptophan synthase mutant Q114A in complex with cesium ion at the metal coordination site and 2-aminophenol quinonoid at the enzyme beta site
6VFD · Tryptophan synthase alpha chain: “Tryptophan synthase mutant Q114A in complex with cesium ion at the metal coordination site and 2-aminophenol…”. X-ray diffraction, 4 ligands (SER, 1D0, CS), 8 pockets (best druggability 0.78).…
- PDB
- 6VFD
- 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
- A0A0D6FWC1, A0A5K1VAP1
- Ligands
- SER, 1D0, CS, CL
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 253 | 52% helix, 14% strand | A0A0D6FWC1 |
| B | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 395 | 48% helix, 21% strand | A0A5K1VAP1 |
Ligands and binding sites
- SER · Serine · ligand · 2 copies · chains A, B
- 1D0 · (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]-3-[(2-hydroxyphenyl)amino]propanoic acid · ligand · chains B
- CS · Cesium ion · metal · 3 copies · chains B
- CL · Chloride ion · ion · 16 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 10 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 210 | 0.78 | 0.93 | 42 | 1D0 |
| 2 | 309 | 0.66 | 0.81 | 35 | EDO, CL |
| 3 | 131 | 0.51 | 0.80 | 31 | empty |
| 4 | 109 | 0.42 | 0.77 | 19 | empty |
| 5 | 76 | 0.41 | 0.79 | 19 | SER |
Interfaces
1 interface between chains.
- A–B · 1345 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 6VFD · Tryptophan synthase mutant Q114A in complex with cesium ion at the metal coordination… · 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 A0A0D6FWC1
- Every structure of UniProt A0A5K1VAP1
- Elsewhere: RCSB PDB 6VFD · PDBe 6VFD · UniProt A0A0D6FWC1 · UniProt A0A5K1VAP1
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