Research workbench
Crystal structure of VAP2 from crotalus atrox venom (form 2-2 crystal)
Analyse Crystal structure of VAP2 from crotalus atrox venom (form 2-2 crystal) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DW1
- Type
- protein
- Length
- 830 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catrocollastatin
- UniProt
- Q90282
- Ligands
- GM6, NAG, MAN, BMA, FUC, CA, ZN
- Pockets
- 10 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Catrocollastatin | protein | 415 | 24% helix, 20% strand | Q90282 |
Ligands and binding sites
- GM6 · 3-(N-hydroxycarboxamido)-2-isobutylpropanoyl-trp-methylamide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · chains A
- BMA · beta-D-mannopyranose · sugar · chains B
- FUC · alpha-L-fucopyranose · sugar · chains B
- CA · Calcium ion · metal · 6 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 691 | 0.66 | 0.75 | 69 | GM6 |
| 2 | 523 | 0.64 | 0.76 | 59 | ZN, GM6 |
| 3 | 288 | 0.56 | 0.76 | 34 | empty |
| 4 | 351 | 0.55 | 0.75 | 41 | empty |
| 5 | 50 | 0.50 | 0.87 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 845 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2DW1 · Crystal structure of VAP2 from Crotalus atrox venom (Form 2-2 crystal) · the same entry in another collection · chain A against A, TM-score 1.00
- Q90282 · AlphaFold monomer V2.0 prediction for zinc metalloproteinase- disintegrin-like VAP2B… · a predicted model of the same protein · chain A against A, TM-score 0.82
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 Q90282
- Elsewhere: RCSB PDB 2DW1 · PDBe 2DW1 · UniProt Q90282
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