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Crystal Structure of T.th.HB8 Branched-Chain Amino Acid Aminotransferase with Pyridoxamine 5'-phosphate
Analyse Crystal Structure of T.th.HB8 Branched-Chain Amino Acid Aminotransferase with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EJ0
- Type
- protein
- Length
- 1,794 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.6
- Source
- Thermus thermophilus
- Molecule
- Branched-chain amino acid aminotransferase
- EC
- 2.6.1.42
- UniProt
- Q5SM19
- Ligands
- PMP
- Pockets
- 17 · best druggability 0.79
Structure
x-ray diffraction · resolution 1.6 · 5 distinct chains · 31% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 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 | 305 | 32% helix, 29% strand | Q5SM19 |
| D | Branched-chain amino acid aminotransferase (EC 2.6.1.42) | protein | 301 | 31% helix, 30% strand | Q5SM19 |
| E | Branched-chain amino acid aminotransferase (EC 2.6.1.42) | protein | 294 | 31% helix, 31% strand | Q5SM19 |
| F | Branched-chain amino acid aminotransferase (EC 2.6.1.42) | protein | 300 | 32% helix, 29% strand | Q5SM19 |
Ligands and binding sites
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 8 copies · chains A, C, B, D, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1076 | 0.79 | 0.81 | 93 | MPD |
| 2 | 1091 | 0.79 | 0.80 | 90 | MPD |
| 3 | 76 | 0.75 | 0.98 | 12 | empty |
| 4 | 459 | 0.72 | 0.82 | 60 | PMP, MPD |
| 5 | 64 | 0.71 | 0.97 | 34 | empty |
Interfaces
12 interfaces between chains.
- A–E · 2487 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 2482 Ų buried · 26 hydrogen bonds · protein-protein
- C–F · 2474 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 920 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 915 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2EJ0 · Crystal structure of T.TH.HB8 branched-chain amino acid aminotransferase 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 2EJ0 · PDBe 2EJ0 · UniProt Q5SM19
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