MolNFT v1 · #10666 · protein
Crystal structure of eschelichia COLI branched-chain amino acid aminotransferase
1IYD: “Crystal structure of eschelichia COLI branched-chain amino acid aminotransferase”. X-ray diffraction, 2 ligands (PLP, GUA), 8 pockets (best druggability 0.84). MolNFT v1 #10666 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1IYD
- Type
- protein
- Length
- 912 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Branched-chain amino acid aminotransferase
- EC
- 2.6.1.42
- UniProt
- P0AB80
- Ligands
- PLP, GUA
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Branched-chain amino acid aminotransferase (EC 2.6.1.42) | protein | 304 | 30% helix, 28% strand | P0AB80 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 3 copies · chains A, B, C
- GUA · Glutaric acid · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.84 | 0.85 | 96 | empty |
| 2 | 419 | 0.76 | 0.85 | 47 | empty |
| 3 | 178 | 0.73 | 0.90 | 38 | PLP, GUA |
| 4 | 196 | 0.72 | 0.89 | 39 | PLP, GUA |
| 5 | 165 | 0.71 | 0.89 | 39 | PLP, GUA |
Interfaces
3 interfaces between chains.
- B–C · 643 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 625 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 621 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1IYD · Crystal structure of eschelichia COLI branched-chain amino acid aminotransferase · the same entry in another collection · chain A against A, TM-score 1.00
- P0AB80 · AlphaFold monomer V2.0 prediction for branched-chain-amino-acid aminotransferase (P0AB80) · 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 P0AB80
- Elsewhere: RCSB PDB 1IYD · PDBe 1IYD · UniProt P0AB80
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