Research workbench
Structure of the CA2+-bound RABPHILIN3A C2B- SNAP25 complex (C2 space group)
Analyse Structure of the CA2+-bound RABPHILIN3A C2B- SNAP25 complex (C2 space group) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LOB
- Type
- protein
- Length
- 725 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rabphilin-3A; Synaptosomal-associated protein 25
- UniProt
- P47709, P60881
- Ligands
- CA, SO4
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 6 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Rabphilin-3A | protein | 138 | 8% helix, 43% strand | P47709 |
| B | Rabphilin-3A | protein | 139 | 8% helix, 44% strand | P47709 |
| D | Synaptosomal-associated protein 25 | protein | 85 | 87% helix, 0% strand | P60881 |
| E | Synaptosomal-associated protein 25 | protein | 66 | 80% helix, 0% strand | P60881 |
| F | Synaptosomal-associated protein 25 | protein | 88 | 78% helix, 0% strand | P60881 |
| G | Synaptosomal-associated protein 25 | protein | 71 | 70% helix, 0% strand | P60881 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 10 copies · chains A, D, B, C, E, F, G
- GOL · Glycerol · additive · 9 copies · chains A, B, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 744 | 0.74 | 0.80 | 77 | empty |
| 2 | 244 | 0.49 | 0.74 | 37 | empty |
| 3 | 97 | 0.46 | 0.80 | 21 | empty |
| 4 | 59 | 0.32 | 0.76 | 16 | empty |
| 5 | 82 | 0.31 | 0.73 | 17 | empty |
Interfaces
14 interfaces between chains.
- D–F · 1737 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 1312 Ų buried · 11 hydrogen bonds · protein-protein
- F–G · 1307 Ų buried · 13 hydrogen bonds · protein-protein
- E–G · 1065 Ų buried · 3 hydrogen bonds · protein-protein
- B–F · 611 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5LOB · Structure of the Ca2+-bound Rabphilin3A C2B- SNAP25 complex (C2 space group) · the same entry in another collection · chain G against G, TM-score 1.00
- P47709 · AlphaFold monomer V2.0 prediction for rabphilin-3A (P47709) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P60881 · AlphaFold monomer V2.0 prediction for synaptosomal-associated protein 25 (P60881) · a predicted model of the same protein · chain E against A, TM-score 0.86
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 P47709
- Every structure of UniProt P60881
- Elsewhere: RCSB PDB 5LOB · PDBe 5LOB · UniProt P47709 · UniProt P60881
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