MolNFT v1 · #115694 · protein
Human cytosolic 5'-nucleotidase II in complex with N-(9H-purin-6-yl)- 3-(3-pyrrol-1-YLPHENYL)BENZAMIDE
5CR7 · Cytosolic purine 5'-nucleotidase: “Human cytosolic 5'-nucleotidase II in complex with N-(9H-purin-6-yl)- 3-(3-pyrrol-1-YLPHENYL)BENZAMIDE”. X-ray diffraction, 3 ligands (5WO, MG, PO4), 9 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 5CR7
- Type
- protein
- Length
- 913 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytosolic purine 5'-nucleotidase
- EC
- 3.1.3.5
- UniProt
- P49902
- Ligands
- 5WO, MG, PO4
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytosolic purine 5'-nucleotidase (EC 3.1.3.5) | protein | 459 | 40% helix, 19% strand | P49902 |
| B | Cytosolic purine 5'-nucleotidase (EC 3.1.3.5) | protein | 454 | 38% helix, 18% strand | P49902 |
Ligands and binding sites
- 5WO · ~{N}-(7~{H}-purin-6-yl)-3-(3-pyrrol-1-ylphenyl) benzamide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · 11 copies · chains A, B
- ACT · Acetate ion · additive · 10 copies · chains A, 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1094 | 0.83 | 0.84 | 99 | PO4, GOL |
| 2 | 997 | 0.83 | 0.84 | 90 | ACT, PO4, GOL |
| 3 | 425 | 0.77 | 0.86 | 50 | empty |
| 4 | 290 | 0.66 | 0.82 | 29 | PO4, MG |
| 5 | 387 | 0.65 | 0.79 | 48 | 5WO, GOL |
Interfaces
1 interface between chains.
- A–B · 4076 Ų buried · 58 hydrogen bonds · protein-protein
Compared structures
- P49902 · AlphaFold monomer V2.0 prediction for cytosolic purine 5'-nucleotidase (P49902) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P49902
- Elsewhere: RCSB PDB 5CR7 · PDBe 5CR7 · UniProt P49902
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