MolNFT v1 · #137991 · protein
Crystal structure of the primed snare-complexin-synaptotagmin-1 C2B complex
5W5D · Vesicle-associated membrane protein 2: “Crystal structure of the primed snare-complexin-synaptotagmin-1 C2B complex”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.43). MolNFT v1 #137991 on GenesisL1: 3D…
- PDB
- 5W5D
- Type
- protein
- Length
- 406 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vesicle-associated membrane protein 2; Syntaxin-1A; Synaptosomal-associated protein 25…
- UniProt
- P63045, P32851, P60881, P63041, P21707
- Ligands
- MG
- Pockets
- 4 · best druggability 0.43
Structure
x-ray diffraction · 6 distinct chains · 62% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vesicle-associated membrane protein 2 | protein | 38 | 92% helix, 0% strand | P63045 |
| B | Syntaxin-1A | protein | 54 | 96% helix, 0% strand | P32851 |
| C | Synaptosomal-associated protein 25 | protein | 61 | 97% helix, 0% strand | P60881 |
| D | Synaptosomal-associated protein 25 | protein | 54 | 94% helix, 0% strand | P60881 |
| E | Complexin-1 | protein | 47 | 64% helix, 0% strand | P63041 |
| F | Synaptotagmin-1 | protein | 152 | 16% helix, 45% strand | P21707 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains C, D
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 | 131 | 0.43 | 0.76 | 22 | empty |
| 2 | 105 | 0.39 | 0.76 | 26 | empty |
| 3 | 64 | 0.36 | 0.78 | 12 | empty |
| 4 | 58 | 0.30 | 0.75 | 15 | empty |
Interfaces
12 interfaces between chains.
- B–C · 1279 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1168 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 995 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 908 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 535 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5W5D · Crystal structure of the primed SNARE-Complexin-Synaptotagmin-1 C2B complex · the same entry in another collection · chain F against F, TM-score 1.00
- P21707 · AlphaFold monomer V2.0 prediction for synaptotagmin-1 (P21707) · a predicted model of the same protein · chain F against A, TM-score 0.95
- P63045 · AlphaFold monomer V2.0 prediction for vesicle-associated membrane protein 2 (P63045) · a predicted model of the same protein · chain A against A, TM-score 0.81
- P63041 · AlphaFold monomer V2.0 prediction for complexin-1 (P63041) · a predicted model of the same protein · chain E against A, TM-score 0.79
- P32851 · AlphaFold monomer V2.0 prediction for syntaxin-1A (P32851) · a predicted model of the same protein · chain B against A, TM-score 0.77
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 P63045
- Every structure of UniProt P32851
- Every structure of UniProt P60881
- Every structure of UniProt P63041
- Every structure of UniProt P21707
- Elsewhere: RCSB PDB 5W5D · PDBe 5W5D · UniProt P63045 · UniProt P32851 · UniProt P60881 · UniProt P63041 · UniProt P21707
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