Research workbench
Human CX31.3/GJC3 connexin hemichannel in the presence of calcium
Analyse Human CX31.3/GJC3 connexin hemichannel in the presence of calcium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L3U
- Type
- protein
- Length
- 1,206 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gap junction gamma-3 protein
- UniProt
- Q8NFK1
- Ligands
- LMN, CA
- Pockets
- 20 · best druggability 0.58
Structure
electron microscopy · 1 distinct chain · 72% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Gap junction gamma-3 protein | protein | 201 | 72% helix, 6% strand | Q8NFK1 |
Ligands and binding sites
- LMN · Lauryl Maltose Neopentyl Glycol · ligand · 6 copies · chains A, B, F, C, D, E
- CA · Calcium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 225 | 0.58 | 0.79 | 23 | empty |
| 2 | 260 | 0.57 | 0.78 | 33 | empty |
| 3 | 214 | 0.57 | 0.79 | 30 | empty |
| 4 | 248 | 0.56 | 0.77 | 29 | empty |
| 5 | 212 | 0.55 | 0.78 | 31 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1239 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 1238 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 1237 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 1236 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 1234 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 6L3U · Human Cx31.3/GJC3 connexin hemichannel in the presence of calcium · the same entry in another collection · chain F against F, TM-score 1.00
- Q8NFK1 · AlphaFold monomer V2.0 prediction for gap junction gamma-3 protein (Q8NFK1) · a predicted model of the same protein · chain F against A, TM-score 0.91
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 Q8NFK1
- Elsewhere: RCSB PDB 6L3U · PDBe 6L3U · UniProt Q8NFK1
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