Research workbench
Crystal structure of vascular apoptosis-inducing protein- 1(ORTHORHOMBIC crystal form)
Analyse Crystal structure of vascular apoptosis-inducing protein- 1(ORTHORHOMBIC… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ERO
- Type
- protein
- Length
- 852 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vascular apoptosis-inducing protein 1
- Ligands
- NAG, CA, ZN, 3CO
- Pockets
- 12 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Vascular apoptosis-inducing protein 1 | protein | 426 | 25% helix, 18% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- 3CO · Cobalt (III) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.66 | 0.85 | 38 | ZN |
| 2 | 97 | 0.57 | 0.86 | 23 | ZN |
| 3 | 449 | 0.57 | 0.73 | 46 | empty |
| 4 | 175 | 0.44 | 0.74 | 29 | 3CO |
| 5 | 67 | 0.33 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 813 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 35 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2ERO · Crystal structure of vascular apoptosis-inducing protein-1(orthorhombic crystal form) · 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
- Elsewhere: RCSB PDB 2ERO · PDBe 2ERO
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