MolNFT v1 · #34907 · protein
Crystal structure of VIP36 EXOPLASMIC/LUMENAL domain, CA2+/MAN2-bound form
2DUR · Vesicular integral-membrane protein VIP36: “Crystal structure of VIP36 EXOPLASMIC/LUMENAL domain, CA2+/MAN2-bound form”. X-ray diffraction, 3 ligands (MAN, CA, CL), 4 pockets (best druggability 0.41). MolNFT v1 #34907 on GenesisL1…
- PDB
- 2DUR
- Type
- protein
- Length
- 501 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vesicular integral-membrane protein VIP36
- UniProt
- P49256
- Ligands
- MAN, CA, CL
- Pockets
- 4 · best druggability 0.41
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vesicular integral-membrane protein VIP36 | protein | 251 | 7% helix, 43% strand | P49256 |
| B | Vesicular integral-membrane protein VIP36 | protein | 250 | 4% helix, 42% strand | P49256 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 8 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.41 | 0.81 | 19 | CL |
| 2 | 121 | 0.40 | 0.75 | 29 | empty |
| 3 | 75 | 0.36 | 0.77 | 16 | empty |
| 4 | 53 | 0.29 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 735 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2DUR · Crystal structure of VIP36 exoplasmic/lumenal domain, Ca2+/Man2-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 1.00
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 2DUR · PDBe 2DUR · UniProt P49256
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