Research workbench
Crystal structure of cytosolic 5'-nucleotidase iiib (cn-iiib) bound to cytidine
Analyse Crystal structure of cytosolic 5'-nucleotidase iiib (cn-iiib) bound to cytidine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NWI
- Type
- protein
- Length
- 594 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 7-methylguanosine phosphate-specific 5'-nucleotidase
- EC
- 3.1.3.5
- UniProt
- Q9W197
- Ligands
- CTN, MG, CL
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 7-methylguanosine phosphate-specific 5'-nucleotidase (EC 3.1.3.5) | protein | 298 | 44% helix, 18% strand | Q9W197 |
| B | 7-methylguanosine phosphate-specific 5'-nucleotidase (EC 3.1.3.5) | protein | 296 | 43% helix, 18% strand | Q9W197 |
Ligands and binding sites
- CTN · 4-amino-1-beta-D-ribofuranosyl-2(1H)-pyrimidinone · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.80 | 0.84 | 61 | CTN, CL |
| 2 | 594 | 0.70 | 0.79 | 50 | MG, CTN, CL |
| 3 | 86 | 0.35 | 0.74 | 15 | empty |
| 4 | 103 | 0.34 | 0.73 | 15 | empty |
| 5 | 80 | 0.32 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 640 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4NWI · Crystal structure of cytosolic 5'-nucleotidase IIIB (cN-IIIB) bound to cytidine · the same entry in another collection · chain A against A, TM-score 1.00
- Q9W197 · AlphaFold monomer V2.0 prediction for 7-methylguanosine phosphate- specific… · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q9W197
- Elsewhere: RCSB PDB 4NWI · PDBe 4NWI · UniProt Q9W197
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