MolNFT v1 · #161628 · protein
Crystal structure of the beta-hydroxyaspartate aldolase of paracoccus denitrificans
6QKB · D-3-hydroxyaspartate aldolase: “Crystal structure of the beta-hydroxyaspartate aldolase of paracoccus denitrificans”. X-ray diffraction, 2 ligands (PLP, MG), 4 pockets (best druggability 0.66). MolNFT v1 #161628 on GenesisL1: 3D…
- PDB
- 6QKB
- Type
- protein
- Length
- 767 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-3-hydroxyaspartate aldolase
- EC
- 4.1.3.-
- UniProt
- A1B8Z1
- Ligands
- PLP, MG
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-3-hydroxyaspartate aldolase (EC 4.1.3.-) | protein | 384 | 34% helix, 24% strand | A1B8Z1 |
| B | D-3-hydroxyaspartate aldolase (EC 4.1.3.-) | protein | 383 | 35% helix, 23% strand | A1B8Z1 |
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
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.66 | 0.82 | 43 | PLP, MG |
| 2 | 272 | 0.65 | 0.82 | 42 | PLP, MG |
| 3 | 369 | 0.58 | 0.76 | 51 | empty |
| 4 | 71 | 0.33 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2794 Ų buried · 52 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6QKB · Crystal structure of the beta-hydroxyaspartate aldolase of Paracoccus denitrificans · the same entry in another collection · chain A against A, TM-score 1.00
- A1B8Z1 · AlphaFold monomer V2.0 prediction for 3-hydroxy-D-aspartate aldolase (A1B8Z1) · a predicted model of the same protein · chain B 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 A1B8Z1
- Elsewhere: RCSB PDB 6QKB · PDBe 6QKB · UniProt A1B8Z1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.