Research workbench
Crystal structure of VIP36 EXOPLASMIC/LUMENAL domain, metal-free form
Analyse Crystal structure of VIP36 EXOPLASMIC/LUMENAL domain, metal-free form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DUP
- Type
- protein
- Length
- 484 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vesicular integral-membrane protein VIP36
- UniProt
- P49256
- Ligands
- CA, CL
- Pockets
- 5 · best druggability 0.44
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vesicular integral-membrane protein VIP36 | protein | 245 | 4% helix, 46% strand | P49256 |
| B | Vesicular integral-membrane protein VIP36 | protein | 239 | 3% helix, 43% strand | P49256 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.44 | 0.81 | 19 | CL |
| 2 | 157 | 0.42 | 0.74 | 31 | empty |
| 3 | 97 | 0.37 | 0.76 | 25 | empty |
| 4 | 50 | 0.37 | 0.81 | 17 | GOL |
| 5 | 52 | 0.32 | 0.77 | 20 | GOL |
Interfaces
1 interface between chains.
- A–B · 724 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2DUP · Crystal structure of VIP36 exoplasmic/lumenal domain, metal-free form · the same entry in another collection · chain A against A, TM-score 1.00
- P49256 · AlphaFold monomer V2.0 prediction for vesicular integral-membrane protein VIP36 (P49256) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P49256
- Elsewhere: RCSB PDB 2DUP · PDBe 2DUP · UniProt P49256
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