Research workbench
Sheep Connexin-50 at 2.5 angstroms reoslution, Lipid Class 2
Analyse Sheep Connexin-50 at 2.5 angstroms reoslution, Lipid Class 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JM9
- Type
- protein
- Length
- 2,328 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Ovis aries
- Molecule
- Gap junction alpha-8 protein
- UniProt
- P55917
- Ligands
- MC3
- Pockets
- 20 · best druggability 0.64
Structure
electron microscopy · resolution 2.5 · 1 distinct chain · 71% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Gap junction alpha-8 protein | protein | 194 | 71% helix, 5% strand | P55917 |
Ligands and binding sites
- MC3 · 1,2-dimyristoyl-rac-glycero-3-phosphocholine · ligand · 168 copies · chains A, F, B, C, D, E, G, L, H, I, J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 437 | 0.64 | 0.77 | 43 | empty |
| 2 | 415 | 0.63 | 0.77 | 41 | empty |
| 3 | 414 | 0.63 | 0.77 | 43 | empty |
| 4 | 385 | 0.63 | 0.77 | 34 | empty |
| 5 | 411 | 0.63 | 0.77 | 43 | empty |
Interfaces
24 interfaces between chains.
- J–K · 1409 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 1409 Ų buried · 12 hydrogen bonds · protein-protein
- I–J · 1409 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1408 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1407 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide (disulfide).
Compared structures
- 7JM9 · Sheep connexin-50 at 2.5 ångströms reoslution, lipid class 2 · the same entry in another collection · chain L against L, TM-score 1.00
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 P55917
- Elsewhere: RCSB PDB 7JM9 · PDBe 7JM9 · UniProt P55917
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