Research workbench
Crystal structure of GENB1 from micromonospora echinospora in complex with plp (internal aldimine)
Analyse Crystal structure of GENB1 from micromonospora echinospora in complex with plp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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