MolNFT v1 · #34904 · protein
Crystal structure of VIP36 EXOPLASMIC/LUMENAL domain, CA2+- bound form
2DUO · Vesicular integral-membrane protein VIP36: “Crystal structure of VIP36 EXOPLASMIC/LUMENAL domain, CA2+- bound form”. X-ray diffraction, 2 ligands (CA, CL), 3 pockets (best druggability 0.43). MolNFT v1 #34904 on GenesisL1: 3D…
- PDB
- 2DUO
- Type
- protein
- Length
- 488 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
- 3 · best druggability 0.43
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vesicular integral-membrane protein VIP36 | protein | 245 | 5% helix, 44% strand | P49256 |
| B | Vesicular integral-membrane protein VIP36 | protein | 243 | 4% helix, 45% strand | P49256 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 153 | 0.43 | 0.75 | 42 | empty |
| 2 | 56 | 0.42 | 0.82 | 19 | CL |
| 3 | 78 | 0.39 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 748 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2DUO · Crystal structure of VIP36 exoplasmic/lumenal domain, Ca2+-bound 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 2DUO · PDBe 2DUO · UniProt P49256
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