Research workbench
Transaminase of gamma-proteobacterium
Analyse Transaminase of gamma-proteobacterium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7P3T
- Type
- protein
- Length
- 1,772 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
- B8KQT8
- Ligands
- PLP
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Branched-chain amino acid aminotransferase (EC 2.6.1.42) | protein | 296 | 28% helix, 29% strand | B8KQT8 |
| B | Branched-chain amino acid aminotransferase (EC 2.6.1.42) | protein | 299 | 27% helix, 28% strand | B8KQT8 |
| C, E, F | Branched-chain amino acid aminotransferase (EC 2.6.1.42) | protein | 294 | 28% helix, 29% strand | B8KQT8 |
| D | Branched-chain amino acid aminotransferase (EC 2.6.1.42) | protein | 295 | 29% helix, 29% strand | B8KQT8 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 6 copies · chains A, E, B, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 229 | 0.85 | 0.98 | 54 | empty |
| 2 | 662 | 0.85 | 0.90 | 131 | GOL |
| 3 | 144 | 0.82 | 0.98 | 37 | empty |
| 4 | 696 | 0.81 | 0.85 | 76 | PLP |
| 5 | 145 | 0.80 | 0.97 | 37 | empty |
Interfaces
12 interfaces between chains.
- B–E · 2359 Ų buried · 36 hydrogen bonds · protein-protein
- D–F · 2352 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 2336 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 723 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 707 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 7P3T · Transaminase of gamma-proteobacterium · 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 B8KQT8
- Elsewhere: RCSB PDB 7P3T · PDBe 7P3T · UniProt B8KQT8
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