MolNFT v1 · #35287 · protein
Crystal structure of VIP36 EXOPLASMIC/LUMENAL domain, CA2+/MAN3GLCNAC- bound form
2E6V · Vesicular integral-membrane protein VIP36: “Crystal structure of VIP36 EXOPLASMIC/LUMENAL domain, CA2+/MAN3GLCNAC- bound form”. X-ray diffraction, 3 ligands (MAN, BMA, CA), 14 pockets (best druggability 0.72). MolNFT v1 #35287 on…
- PDB
- 2E6V
- Type
- protein
- Length
- 1,180 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vesicular integral-membrane protein VIP36
- UniProt
- P49256
- Ligands
- MAN, BMA, CA
- Pockets
- 14 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 5% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vesicular integral-membrane protein VIP36 | protein | 241 | 7% helix, 44% strand | P49256 |
| B | Vesicular integral-membrane protein VIP36 | protein | 237 | 5% helix, 43% strand | P49256 |
| C | Vesicular integral-membrane protein VIP36 | protein | 236 | 4% helix, 44% strand | P49256 |
| D | Vesicular integral-membrane protein VIP36 | protein | 237 | 5% helix, 44% strand | P49256 |
| E | Vesicular integral-membrane protein VIP36 | protein | 229 | 4% helix, 46% strand | P49256 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B, C
- CA · Calcium ion · metal · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 79 | 0.72 | 0.95 | 17 | empty |
| 2 | 375 | 0.62 | 0.78 | 45 | MAN |
| 3 | 161 | 0.54 | 0.80 | 34 | empty |
| 4 | 179 | 0.53 | 0.79 | 33 | empty |
| 5 | 206 | 0.50 | 0.76 | 31 | empty |
Interfaces
5 interfaces between chains.
- A–B · 775 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 660 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 502 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 287 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 186 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 2E6V · Crystal structure of VIP36 exoplasmic/lumenal domain, Ca2+/Man3GlcNAc-bound form · the same entry in another collection · chain E against E, 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 E 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 2E6V · PDBe 2E6V · UniProt P49256
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