Research workbench
Crystal structure of the E130Y mutant of human soluble calcium- activated nucleotidase (scan) with calcium ion
Analyse Crystal structure of the E130Y mutant of human soluble calcium- activated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2H2U
- Type
- protein
- Length
- 632 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble calcium-activated nucleotidase 1
- EC
- 3.6.1.6
- UniProt
- Q8WVQ1
- Ligands
- CA
- Pockets
- 9 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Soluble calcium-activated nucleotidase 1 (EC 3.6.1.6) | protein | 315 | 6% helix, 51% strand | Q8WVQ1 |
| B | Soluble calcium-activated nucleotidase 1 (EC 3.6.1.6) | protein | 317 | 6% helix, 50% strand | Q8WVQ1 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 354 | 0.67 | 0.81 | 27 | empty |
| 2 | 260 | 0.66 | 0.83 | 31 | empty |
| 3 | 215 | 0.62 | 0.82 | 29 | empty |
| 4 | 299 | 0.62 | 0.80 | 28 | empty |
| 5 | 164 | 0.52 | 0.79 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1235 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 2H2U · Crystal structure of the E130Y mutant of human soluble calcium-activated nucleotidase… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8WVQ1 · AlphaFold monomer V2.0 prediction for soluble calcium-activated nucleotidase 1 (Q8WVQ1) · a predicted model of the same protein · 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 Q8WVQ1
- Elsewhere: RCSB PDB 2H2U · PDBe 2H2U · UniProt Q8WVQ1
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