MolNFT v1 · #114982 · protein
Crystal structure of deoxyribose-phosphate aldolase from colwellia psychrerythraea (hexagonal form)
5C5Y: “Crystal structure of deoxyribose-phosphate aldolase from colwellia psychrerythraea (hexagonal form)”. X-ray diffraction, 1 ligand (UNL), 9 pockets (best druggability 0.81). MolNFT v1 #114982 on GenesisL1: 3D structure, binding sites…
- PDB
- 5C5Y
- Type
- protein
- Length
- 986 residues
- Chains
- 4
- 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
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 247 | 49% helix, 15% strand | Q483R4 |
| B | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 246 | 49% helix, 15% strand | Q483R4 |
| C | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 246 | 49% helix, 15% strand | Q483R4 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 661 | 0.81 | 0.86 | 74 | GOL |
| 2 | 202 | 0.64 | 0.84 | 28 | empty |
| 3 | 213 | 0.63 | 0.83 | 30 | empty |
| 4 | 211 | 0.62 | 0.82 | 24 | empty |
| 5 | 234 | 0.60 | 0.80 | 29 | empty |
Interfaces
5 interfaces between chains.
- C–D · 691 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 664 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 316 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 300 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 223 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5C5Y · 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 5C5Y · PDBe 5C5Y · UniProt Q483R4
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