MolNFT v1 · #9187 · protein
5'-nucleotidase (E. COLI) in complex with adenosine and phosphate
1HO5: “5'-nucleotidase (E. COLI) in complex with adenosine and phosphate”. X-ray diffraction, 3 ligands (ADN, MN, PO4), 6 pockets (best druggability 0.76). MolNFT v1 #9187 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1HO5
- Type
- protein
- Length
- 1,050 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-nucleotidase
- EC
- 3.1.3.5, 3.6.1.45
- UniProt
- P07024
- Ligands
- ADN, MN, PO4
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 5'-nucleotidase (EC 3.1.3.5, 3.6.1.45) | protein | 525 | 30% helix, 29% strand | P07024 |
Ligands and binding sites
- ADN · Adenosine · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 964 | 0.76 | 0.79 | 104 | PO4, ADN |
| 2 | 839 | 0.75 | 0.79 | 89 | PO4, ADN |
| 3 | 275 | 0.53 | 0.75 | 52 | empty |
| 4 | 106 | 0.43 | 0.78 | 24 | empty |
| 5 | 60 | 0.42 | 0.81 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 379 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
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 P07024
- Elsewhere: RCSB PDB 1HO5 · PDBe 1HO5 · UniProt P07024
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