MolNFT v1 · #150136 · protein
Crystal structure of branched-chain amino acid aminotransferase from thermobaculum terrenum in plp-form (holo-form)
6GKR · Branched-chain-amino-acid aminotransferase: “Crystal structure of branched-chain amino acid aminotransferase from thermobaculum terrenum in plp-form…”. X-ray diffraction, 2 ligands (PLP, CL), 12 pockets (best druggability 0.70).…
- PDB
- 6GKR
- Type
- protein
- Length
- 920 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
- D1CCW1
- Ligands
- PLP, CL
- Pockets
- 12 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Branched-chain-amino-acid aminotransferase (EC 2.6.1.42) | protein | 307 | 30% helix, 30% strand | D1CCW1 |
| B | Branched-chain-amino-acid aminotransferase (EC 2.6.1.42) | protein | 307 | 30% helix, 30% strand | D1CCW1 |
| C | Branched-chain-amino-acid aminotransferase (EC 2.6.1.42) | protein | 306 | 30% helix, 29% strand | D1CCW1 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 384 | 0.70 | 0.82 | 56 | PLP, CL |
| 2 | 367 | 0.67 | 0.81 | 53 | PLP, CL |
| 3 | 386 | 0.67 | 0.80 | 35 | empty |
| 4 | 201 | 0.58 | 0.80 | 42 | PLP |
| 5 | 193 | 0.57 | 0.80 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2517 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 679 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 500 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6GKR · Crystal structure of branched-chain amino acid aminotransferase from Thermobaculum… · 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 D1CCW1
- Elsewhere: RCSB PDB 6GKR · PDBe 6GKR · UniProt D1CCW1
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