Research workbench
Molecular basis for multiple ligand binding of calsequestrin and potential inhibition by caffeine and gallocatecin
Analyse Molecular basis for multiple ligand binding of calsequestrin and potential… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V1W
- Type
- protein
- Length
- 349 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calsequestrin-1
- UniProt
- P07221
- Ligands
- NAG, CA, NA
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calsequestrin-1 | protein | 349 | 39% helix, 19% strand | P07221 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- CA · Calcium ion · metal · 4 copies · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 150 | 0.71 | 0.90 | 19 | empty |
| 2 | 106 | 0.47 | 0.79 | 17 | MPD |
| 3 | 141 | 0.40 | 0.74 | 26 | NA |
| 4 | 91 | 0.37 | 0.76 | 18 | empty |
| 5 | 83 | 0.35 | 0.75 | 14 | MPD |
Modifications
Observed in the structure: 1 glycan (N-glycosylation).
Compared structures
- 3V1W · Molecular Basis for Multiple Ligand Binding of Calsequestrin and Potential Inhibition by… · the same entry in another collection · chain A against A, TM-score 1.00
- P07221 · AlphaFold monomer V2.0 prediction for calsequestrin-1 (P07221) · a predicted model of the same protein · chain A 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 P07221
- Elsewhere: RCSB PDB 3V1W · PDBe 3V1W · UniProt P07221
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