MolNFT v1 · #33417 · protein
Structural basis for a MUNC13-1 homodimer - MUNC13-1 - rim heterodimer switch: C2-domains as versatile protein-protein interaction modules
2CJT · Unc-13 homolog a: “Structural basis for a MUNC13-1 homodimer - MUNC13-1 - rim heterodimer switch: C2-domains as versatile…”. X-ray diffraction, 7 pockets (best druggability 0.74). MolNFT v1 #33417 on GenesisL1: 3D structure, binding…
- PDB
- 2CJT
- Type
- protein
- Length
- 496 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Unc-13 homolog a
- UniProt
- Q62768
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 60% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Unc-13 homolog a | protein | 121 | 5% helix, 55% strand | Q62768 |
| C, D | Unc-13 homolog a | protein | 127 | 5% helix, 65% strand | Q62768 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 23 copies · chains A, D, C, B
- FMT · Formic acid · additive · 11 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 674 | 0.74 | 0.80 | 48 | empty |
| 2 | 521 | 0.73 | 0.81 | 45 | empty |
| 3 | 734 | 0.70 | 0.77 | 59 | EDO, FMT |
| 4 | 164 | 0.45 | 0.76 | 32 | EDO, FMT |
| 5 | 66 | 0.31 | 0.75 | 15 | empty |
Interfaces
4 interfaces between chains.
- B–D · 702 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 662 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 149 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 112 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2CJT · Structural Basis for a Munc13-1 Homodimer - Munc13-1 - RIM Heterodimer Switch: C2-domains… · the same entry in another collection · chain A against A, TM-score 1.00
- Q62768 · AlphaFold monomer V2.0 prediction for protein unc-13 homolog a (Q62768) · a predicted model of the same protein · chain C 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 Q62768
- Elsewhere: RCSB PDB 2CJT · PDBe 2CJT · UniProt Q62768
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