MolNFT v1 · #146634 · protein
Cryo-EM structure of the mitochondrial calcium uniporter mcu from the fungus cyphellophora europaea
6DNF: “Cryo-EM structure of the mitochondrial calcium uniporter mcu from the fungus cyphellophora europaea”. Electron microscopy, 2 ligands (DGG, CA), 13 pockets (best druggability 0.69). MolNFT v1 #146634 on GenesisL1: 3D structure…
- PDB
- 6DNF
- Type
- protein
- Length
- 900 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitochondrial calcium uniporter mcu
- UniProt
- W2SDE2
- Ligands
- DGG, CA
- Pockets
- 13 · best druggability 0.69
Structure
electron microscopy · 1 distinct chain · 56% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Mitochondrial calcium uniporter mcu | protein | 225 | 56% helix, 13% strand | W2SDE2 |
Ligands and binding sites
- DGG · 1-[glycerolylphosphonyl]-2-[8-(2-hexyl-cyclopropyl)-octanal-1-yl]-3-[hexadecanal-1-yl]-glycerol · ligand · 8 copies · chains A, D, B, C
- CA · Calcium ion · metal · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 673 | 0.69 | 0.77 | 49 | empty |
| 2 | 75 | 0.68 | 0.93 | 19 | empty |
| 3 | 70 | 0.66 | 0.92 | 20 | empty |
| 4 | 433 | 0.61 | 0.75 | 32 | DGG, CA |
| 5 | 277 | 0.60 | 0.79 | 24 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1483 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1467 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1098 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 1086 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 30 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6DNF · Cryo-EM structure of the mitochondrial calcium uniporter MCU from the fungus… · the same entry in another collection · chain A against A, 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 W2SDE2
- Elsewhere: RCSB PDB 6DNF · PDBe 6DNF · UniProt W2SDE2
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