MolNFT v1 · #178812 · protein
Sheep connexin-50 at 2.5 ångströms resolution, lipid class 3
7JMC · Gap junction alpha-8 protein: “Sheep connexin-50 at 2.5 ångströms resolution, lipid class 3”. Electron microscopy, 1 ligand (MC3), 20 pockets (best druggability 0.64). MolNFT v1 #178812 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7JMC
- Type
- protein
- Length
- 2,304 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gap junction alpha-8 protein
- UniProt
- P55917
- Ligands
- MC3
- Pockets
- 20 · best druggability 0.64
Structure
electron microscopy · 1 distinct chain · 73% 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 | 192 | 73% helix, 5% strand | P55917 |
Ligands and binding sites
- MC3 · 1,2-dimyristoyl-rac-glycero-3-phosphocholine · ligand · 144 copies · chains A, B, F, C, D, E, G, H, L, 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 | 448 | 0.64 | 0.77 | 39 | empty |
| 2 | 387 | 0.63 | 0.78 | 32 | empty |
| 3 | 400 | 0.63 | 0.77 | 31 | empty |
| 4 | 395 | 0.63 | 0.77 | 31 | empty |
| 5 | 397 | 0.62 | 0.77 | 31 | empty |
Interfaces
24 interfaces between chains.
- C–D · 1393 Ų buried · 13 hydrogen bonds · protein-protein
- K–L · 1391 Ų buried · 13 hydrogen bonds · protein-protein
- I–J · 1391 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1391 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 1389 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide (disulfide).
Compared structures
- 7JMC · Sheep Connexin-50 at 2.5 angstroms resolution, Lipid Class 3 · 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 7JMC · PDBe 7JMC · UniProt P55917
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