MolNFT v1 · #114877 · protein
Crystal structure of deoxyribose-phosphate aldolase from colwellia psychrerythraea (tetragonal form)
5C2X: “Crystal structure of deoxyribose-phosphate aldolase from colwellia psychrerythraea (tetragonal form)”. X-ray diffraction, 3 ligands (UNL, SO4, CO3), 4 pockets (best druggability 0.62). MolNFT v1 #114877 on GenesisL1: 3D structure…
- PDB
- 5C2X
- Type
- protein
- Length
- 492 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyribose-phosphate aldolase
- EC
- 4.1.2.4
- UniProt
- Q483R4
- Ligands
- UNL, SO4, CO3
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 246 | 50% helix, 15% strand | Q483R4 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- CO3 · Carbonate ion · ion · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.62 | 0.82 | 29 | empty |
| 2 | 242 | 0.60 | 0.80 | 28 | empty |
| 3 | 104 | 0.44 | 0.78 | 24 | UNL, SO4 |
| 4 | 96 | 0.41 | 0.78 | 21 | UNL, SO4 |
Interfaces
1 interface between chains.
- A–B · 655 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5C2X · Crystal structure of deoxyribose-phosphate aldolase from Colwellia psychrerythraea… · 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 Q483R4
- Elsewhere: RCSB PDB 5C2X · PDBe 5C2X · UniProt Q483R4
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