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Cryo-EM structure of the mitochondrial calcium uniporter from N. fischeri bound to saposin
Analyse Cryo-EM structure of the mitochondrial calcium uniporter from N. fischeri bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D80
- Type
- protein
- Length
- 1,568 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Saposin a; Mitochondrial calcium uniporter
- UniProt
- A1CWT6
- Ligands
- CA
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 6 distinct chains · 57% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F, I | Saposin a | protein | 81 | 85% helix, 0% strand | — |
| H, G, J | Saposin a | protein | 80 | 75% helix, 0% strand | — |
| K | Saposin a | protein | 79 | 84% helix, 0% strand | — |
| A | Mitochondrial calcium uniporter | protein | 275 | 49% helix, 11% strand | A1CWT6 |
| B, D | Mitochondrial calcium uniporter | protein | 269 | 53% helix, 10% strand | A1CWT6 |
| C | Mitochondrial calcium uniporter | protein | 274 | 49% helix, 14% strand | A1CWT6 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.76 | 0.79 | 78 | empty |
| 2 | 891 | 0.74 | 0.78 | 63 | empty |
| 3 | 718 | 0.72 | 0.78 | 70 | empty |
| 4 | 569 | 0.66 | 0.76 | 47 | empty |
| 5 | 410 | 0.58 | 0.75 | 42 | empty |
Interfaces
20 interfaces between chains.
- C–D · 1710 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1703 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1436 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 1426 Ų buried · 8 hydrogen bonds · protein-protein
- H–G · 160 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6D80 · Cryo-EM structure of the mitochondrial calcium uniporter from N. fischeri bound to saposin · the same entry in another collection · chain F against F, 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 A1CWT6
- Elsewhere: RCSB PDB 6D80 · PDBe 6D80 · UniProt A1CWT6
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