MolNFT v1 · #141456 · protein
Crystal structure of GENB1 from micromonospora echinospora in complex with plp (internal aldimine)
5Z83 · C-6' aminotransferase: “Crystal structure of GENB1 from micromonospora echinospora in complex with plp (internal aldimine)”. X-ray diffraction, 2 ligands (PLP, MG), 8 pockets (best druggability 0.75). MolNFT v1 #141456 on GenesisL1…
- PDB
- 5Z83
- 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, MG
- Pockets
- 8 · best druggability 0.75
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
- MG · Magnesium ion · metal · 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 | 80 | 0.75 | 0.98 | 28 | empty |
| 2 | 545 | 0.75 | 0.83 | 65 | PLP, MG |
| 3 | 533 | 0.75 | 0.82 | 66 | PLP, MG |
| 4 | 64 | 0.71 | 0.97 | 24 | empty |
| 5 | 394 | 0.67 | 0.80 | 52 | empty |
Interfaces
1 interface between chains.
- A–B · 3416 Ų buried · 53 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5Z83 · Crystal structure of GenB1 from Micromonospora echinospora in complex with PLP (internal… · 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 5Z83 · PDBe 5Z83 · UniProt Q70KD9
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