MolNFT v1 · #179635 · protein
1.60 ångström resolution crystal structure of the beta-Q114A mutant of tryptophan synthase in complex with N-(4'- trifluoromethoxybenzenesulfonyl)-2-amino-1-ethylphosphate (F9F) at the enzyme alpha-site, cesium ion at the metal coordination site, and 2-aminophenol quinonoid at the enzyme beta site
7KBN · Tryptophan synthase alpha chain: “1.60 ångström resolution crystal structure of the beta-Q114A mutant of tryptophan synthase in complex with…”. X-ray diffraction, 5 ligands (F9F, 1D0, 2AF), 9 pockets (best druggability 0.83). MolNFT…
- PDB
- 7KBN
- Type
- protein
- Length
- 663 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
- F9F, 1D0, 2AF, CS, CL
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tryptophan synthase alpha chain (EC 4.2.1.20) | protein | 268 | 50% helix, 14% strand | P00929 |
| B | Tryptophan synthase beta chain (EC 4.2.1.20) | protein | 395 | 47% helix, 22% strand | P0A2K1 |
Ligands and binding sites
- F9F · 2-({[4-(trifluoromethoxy)phenyl]sulfonyl}amino)ethyl dihydrogen phosphate · ligand · 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
- 2AF · 2-aminophenol · ligand · chains B
- CS · Cesium ion · metal · 2 copies · chains B
- CL · Chloride ion · ion · 7 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 19 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 170 | 0.83 | 0.97 | 45 | F9F |
| 2 | 123 | 0.79 | 0.98 | 35 | 1D0 |
| 3 | 99 | 0.45 | 0.79 | 20 | CL |
| 4 | 74 | 0.41 | 0.79 | 15 | EDO |
| 5 | 102 | 0.38 | 0.75 | 20 | DMS |
Interfaces
1 interface between chains.
- A–B · 1411 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 7KBN · 1.60 Angstrom resolution crystal structure of the beta-Q114A mutant of Tryptophan… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A2K1 · AlphaFold monomer V2.0 prediction for tryptophan synthase beta chain (P0A2K1) · a predicted model of the same protein · chain B 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 P0A2K1
- Elsewhere: RCSB PDB 7KBN · PDBe 7KBN · UniProt P00929 · UniProt P0A2K1
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