Research workbench
Structural basis for a MUNC13-1 homodimer - MUNC13-1 - rim heterodimer switch: C2-domains as versatile protein-protein interaction modules
Analyse Structural basis for a MUNC13-1 homodimer - MUNC13-1 - rim heterodimer switch… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CJS
- Type
- protein
- Length
- 373 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Unc-13 homolog a; Regulating synaptic membrane exocytosis protein 2
- UniProt
- Q62768, Q9JIS1
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Unc-13 homolog a | protein | 163 | 15% helix, 52% strand | Q62768 |
| B | Unc-13 homolog a | protein | 156 | 11% helix, 54% strand | Q62768 |
| C | Regulating synaptic membrane exocytosis protein 2 | protein | 54 | 13% helix, 35% strand | Q9JIS1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains C
- GOL · Glycerol · additive · 6 copies · chains A, C, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 524 | 0.76 | 0.83 | 65 | EDO, GOL |
| 2 | 152 | 0.52 | 0.79 | 27 | empty |
| 3 | 147 | 0.52 | 0.79 | 20 | empty |
| 4 | 71 | 0.32 | 0.74 | 14 | GOL |
| 5 | 65 | 0.31 | 0.74 | 15 | GOL |
Interfaces
3 interfaces between chains.
- A–C · 1320 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 552 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 536 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2CJS · Structural Basis for a Munc13-1 Homodimer - Munc13-1 - RIM Heterodimer Switch: C2-domains… · the same entry in another collection · chain C against C, TM-score 1.00
- Q9JIS1 · AlphaFold monomer V2.0 prediction for regulating synaptic membrane exocytosis protein 2… · a predicted model of the same protein · chain C against A, TM-score 0.85
- Q62768 · AlphaFold monomer V2.0 prediction for protein unc-13 homolog a (Q62768) · a predicted model of the same protein · chain B against A, TM-score 0.83
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 Q62768
- Every structure of UniProt Q9JIS1
- Elsewhere: RCSB PDB 2CJS · PDBe 2CJS · UniProt Q62768 · UniProt Q9JIS1
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