MolNFT v1 · #141470 · protein
Crystal structure of an aminotransferase in complex with product-1
5Z8K · C-6' aminotransferase: “Crystal structure of an aminotransferase in complex with product-1”. X-ray diffraction, 2 ligands (PLP, XXX), 8 pockets (best druggability 0.76). MolNFT v1 #141470 on GenesisL1: 3D structure, binding sites…
- PDB
- 5Z8K
- Type
- protein
- Length
- 816 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-6' aminotransferase
- UniProt
- Q70KD9
- Ligands
- PLP, XXX
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | C-6' aminotransferase | protein | 408 | 42% helix, 16% strand | Q70KD9 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- XXX · (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2, 6-diamino-2,6-dideoxy-alpha-D-glucopyranoside · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 531 | 0.76 | 0.83 | 63 | PLP, XXX |
| 2 | 551 | 0.75 | 0.83 | 58 | PLP, XXX |
| 3 | 67 | 0.73 | 0.98 | 27 | empty |
| 4 | 66 | 0.72 | 0.97 | 27 | empty |
| 5 | 410 | 0.67 | 0.80 | 57 | empty |
Interfaces
1 interface between chains.
- A–B · 3438 Ų buried · 54 hydrogen bonds · protein-protein
Compared structures
- 5Z8K · Crystal structure of an aminotransferase in complex with product-1 · 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 Q70KD9
- Elsewhere: RCSB PDB 5Z8K · PDBe 5Z8K · UniProt Q70KD9
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