Research workbench
Crystal structure of T.TH.HB8 branched-chain amino acid aminotransferase complexed with N-(5'-phosphopyridoxyl)-L-glutamate
Analyse Crystal structure of T.TH.HB8 branched-chain amino acid aminotransferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EJ2
- Type
- protein
- Length
- 1,793 residues
- Chains
- 6
- 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
- PPE
- Pockets
- 19 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 31% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Branched-chain amino acid aminotransferase (EC 2.6.1.42) | protein | 294 | 31% helix, 30% strand | Q5SM19 |
| B | Branched-chain amino acid aminotransferase (EC 2.6.1.42) | protein | 305 | 32% helix, 28% strand | Q5SM19 |
| C | Branched-chain amino acid aminotransferase (EC 2.6.1.42) | protein | 297 | 31% helix, 31% strand | Q5SM19 |
| D | Branched-chain amino acid aminotransferase (EC 2.6.1.42) | protein | 301 | 31% helix, 30% strand | Q5SM19 |
| E, F | Branched-chain amino acid aminotransferase (EC 2.6.1.42) | protein | 298 | 31% helix, 30% strand | Q5SM19 |
Ligands and binding sites
- PPE · 4-[(1,3-dicarboxy-propylamino)-methyl]-3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridinium · ligand · 6 copies · chains A, E, B, D, C, F
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.79 | 0.81 | 95 | empty |
| 2 | 1116 | 0.78 | 0.80 | 97 | empty |
| 3 | 90 | 0.76 | 0.97 | 15 | empty |
| 4 | 369 | 0.71 | 0.83 | 52 | PPE |
| 5 | 59 | 0.71 | 0.98 | 31 | empty |
Interfaces
12 interfaces between chains.
- A–E · 2492 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 2484 Ų buried · 27 hydrogen bonds · protein-protein
- C–F · 2483 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 906 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 906 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2EJ2 · 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 2EJ2 · PDBe 2EJ2 · UniProt Q5SM19
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