Research workbench
Structure of calm (picalm) in complex with VAMP8
Analyse Structure of calm (picalm) in complex with VAMP8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZYM
- Type
- protein
- Length
- 836 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol-binding clathrin assembly protein, vesicle-associated membrane…
- UniProt
- O55012, O70404
- Ligands
- PO4
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphatidylinositol-binding clathrin assembly protein, vesicle-associated membrane protein 8 | protein | 278 | 76% helix, 0% strand | O55012, O70404 |
| C | Phosphatidylinositol-binding clathrin assembly protein, vesicle-associated membrane protein 8 | protein | 280 | 75% helix, 0% strand | O55012, O70404 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 7 copies · chains A, C, B
- GOL · Glycerol · additive · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 724 | 0.71 | 0.78 | 67 | PO4 |
| 2 | 138 | 0.44 | 0.76 | 29 | empty |
| 3 | 136 | 0.42 | 0.75 | 25 | empty |
| 4 | 88 | 0.35 | 0.74 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1118 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 438 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3ZYM · Structure of CALM (PICALM) in complex with VAMP8 · the same entry in another collection · chain C against C, TM-score 1.00
- O55012 · AlphaFold monomer V2.0 prediction for phosphatidylinositol-binding clathrin assembly… · a predicted model of the same protein · chain A against A, TM-score 0.94
- O70404 · AlphaFold monomer V2.0 prediction for vesicle-associated membrane protein 8 (O70404) · a predicted model of the same protein · chain A against A, TM-score 0.14
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 O55012
- Every structure of UniProt O70404
- Elsewhere: RCSB PDB 3ZYM · PDBe 3ZYM · UniProt O55012 · UniProt O70404
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