Research workbench
Crystal structure of vascular apoptosis-inducing protein-1(TETRAGONAL crystal form)
Analyse Crystal structure of vascular apoptosis-inducing protein-1(TETRAGONAL crystal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ERQ
- Type
- protein
- Length
- 847 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
- Pockets
- 11 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vascular apoptosis-inducing protein 1 | protein | 424 | 26% helix, 17% strand | — |
| B | Vascular apoptosis-inducing protein 1 | protein | 423 | 25% helix, 17% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
- CA · Calcium ion · metal · 4 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
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 181 | 0.65 | 0.85 | 37 | ZN |
| 2 | 105 | 0.59 | 0.86 | 23 | ZN |
| 3 | 257 | 0.51 | 0.74 | 30 | empty |
| 4 | 147 | 0.44 | 0.75 | 28 | empty |
| 5 | 79 | 0.39 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 849 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 35 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2ERQ · Crystal structure of vascular apoptosis-inducing protein-1(tetragonal 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 2ERQ · PDBe 2ERQ
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