MolNFT v1 · #35696 · protein
Crystal structure of T.TH.HB8 branched-chain amino acid aminotransferase complexed with gabapentin
2EJ3: “Crystal structure of T.TH.HB8 branched-chain amino acid aminotransferase complexed with gabapentin”. X-ray diffraction, 2 ligands (PLP, GBN), 11 pockets (best druggability 0.79). MolNFT v1 #35696 on GenesisL1: 3D structure, binding…
- PDB
- 2EJ3
- 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, GBN
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Branched-chain amino acid aminotransferase (EC 2.6.1.42) | protein | 297 | 31% helix, 29% strand | Q5SM19 |
| B | Branched-chain amino acid aminotransferase (EC 2.6.1.42) | protein | 304 | 33% helix, 29% strand | Q5SM19 |
| C | Branched-chain amino acid aminotransferase (EC 2.6.1.42) | protein | 294 | 31% helix, 29% strand | Q5SM19 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 3 copies · chains A, B, C
- GBN · [1-(aminomethyl)cyclohexyl]acetic 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
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1171 | 0.79 | 0.80 | 99 | MPD |
| 2 | 347 | 0.63 | 0.79 | 50 | PLP, GBN |
| 3 | 177 | 0.58 | 0.82 | 29 | PLP, GBN |
| 4 | 161 | 0.57 | 0.82 | 31 | PLP, GBN |
| 5 | 162 | 0.43 | 0.73 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–C · 907 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 897 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 873 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 2EJ3 · 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 2EJ3 · PDBe 2EJ3 · UniProt Q5SM19
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