MolNFT v1 · #35691 · protein
Crystal structure of T.TH.HB8 branched-chain amino acid aminotransferase complexed with 4-methylvaleric acid
2EIY: “Crystal structure of T.TH.HB8 branched-chain amino acid aminotransferase complexed with 4-methylvaleric acid”. X-ray diffraction, 2 ligands (PLP, 4MV), 13 pockets (best druggability 0.78). MolNFT v1 #35691 on GenesisL1: 3D…
- PDB
- 2EIY
- Type
- protein
- Length
- 895 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
- Q5SM19
- Ligands
- PLP, 4MV
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Branched-chain amino acid aminotransferase (EC 2.6.1.42) | protein | 297 | 31% helix, 28% strand | Q5SM19 |
| B | Branched-chain amino acid aminotransferase (EC 2.6.1.42) | protein | 304 | 32% helix, 27% strand | Q5SM19 |
| C | Branched-chain amino acid aminotransferase (EC 2.6.1.42) | protein | 294 | 31% helix, 30% strand | Q5SM19 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 3 copies · chains A, B, C
- 4MV · 4-methyl valeric acid · ligand · 3 copies · chains A, B, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1131 | 0.78 | 0.80 | 91 | MPD |
| 2 | 359 | 0.63 | 0.79 | 52 | PLP, 4MV |
| 3 | 160 | 0.58 | 0.83 | 31 | PLP, 4MV |
| 4 | 184 | 0.57 | 0.81 | 29 | PLP, 4MV |
| 5 | 168 | 0.45 | 0.75 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–C · 909 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 901 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 870 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 2EIY · Crystal Structure of T.th.HB8 Branched-Chain Amino Acid Aminotransferase Complexed with… · 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 Q5SM19
- Elsewhere: RCSB PDB 2EIY · PDBe 2EIY · UniProt Q5SM19
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