MolNFT v1 · #19394 · protein
Crystal structure of 7,8-diaminopelargonic acid synthase in complex with 7-keto-8-aminopelargonic acid
1QJ3: “Crystal structure of 7,8-diaminopelargonic acid synthase in complex with 7-keto-8-aminopelargonic acid”. X-ray diffraction, 3 ligands (PLP, KAP, NA), 1 pocket (best druggability 0.82). MolNFT v1 #19394 on GenesisL1: 3D structure…
- PDB
- 1QJ3
- Type
- protein
- Length
- 831 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 7,8-diaminopelargonic acid synthase
- EC
- 2.6.1.62
- UniProt
- P12995
- Ligands
- PLP, KAP, NA
- Pockets
- 1 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 7,8-diaminopelargonic acid synthase (EC 2.6.1.62) | protein | 416 | 41% helix, 20% strand | P12995 |
| B | 7,8-diaminopelargonic acid synthase (EC 2.6.1.62) | protein | 415 | 41% helix, 20% strand | P12995 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- KAP · 7-keto-8-aminopelargonic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 974 | 0.82 | 0.83 | 122 | PLP, KAP |
Interfaces
1 interface between chains.
- A–B · 4348 Ų buried · 67 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1QJ3 · Crystal structure of 7,8-diaminopelargonic acid synthase in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P12995 · AlphaFold monomer V2.0 prediction for adenosylmethionine-8-amino-7-oxononanoate… · a predicted model of the same protein · 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 P12995
- Elsewhere: RCSB PDB 1QJ3 · PDBe 1QJ3 · UniProt P12995
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.