Research workbench
Crystal structure of 5'-nucleotidase from candida albicans SC5314
Analyse Crystal structure of 5'-nucleotidase from candida albicans SC5314 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C9F
- Type
- protein
- Length
- 1,071 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-nucleotidase
- UniProt
- Q5A5Q7
- Ligands
- NA, ZN
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-nucleotidase | protein | 531 | 30% helix, 24% strand | Q5A5Q7 |
| B | 5'-nucleotidase | protein | 540 | 28% helix, 24% strand | Q5A5Q7 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- FMT · Formic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 969 | 0.77 | 0.80 | 79 | FMT |
| 2 | 544 | 0.73 | 0.81 | 59 | NA |
| 3 | 333 | 0.72 | 0.85 | 49 | NA, FMT |
| 4 | 428 | 0.71 | 0.82 | 49 | NA |
| 5 | 143 | 0.59 | 0.83 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1145 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 3C9F · Crystal structure of 5'-nucleotidase from Candida albicans SC5314 · 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 Q5A5Q7
- Elsewhere: RCSB PDB 3C9F · PDBe 3C9F · UniProt Q5A5Q7
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