Research workbench
Structure of calcium-bound regulatory domain of the human ATP-Mg/Pi carrier in the P212121 form
Analyse Structure of calcium-bound regulatory domain of the human ATP-Mg/Pi carrier in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZCV
- Type
- protein
- Length
- 603 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Homo sapiens
- Molecule
- Calcium-binding mitochondrial carrier protein SCaMC-1
- UniProt
- Q6NUK1
- Ligands
- CA, SO4
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · resolution 2.8 · 4 distinct chains · 60% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calcium-binding mitochondrial carrier protein SCaMC-1 | protein | 154 | 58% helix, 5% strand | Q6NUK1 |
| B | Calcium-binding mitochondrial carrier protein SCaMC-1 | protein | 152 | 60% helix, 5% strand | Q6NUK1 |
| C | Calcium-binding mitochondrial carrier protein SCaMC-1 | protein | 151 | 60% helix, 4% strand | Q6NUK1 |
| D | Calcium-binding mitochondrial carrier protein SCaMC-1 | protein | 146 | 62% helix, 5% strand | Q6NUK1 |
Ligands and binding sites
- CA · Calcium ion · metal · 13 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 6 copies · chains A, C, B, D
- GOL · Glycerol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 491 | 0.74 | 0.83 | 69 | SO4 |
| 2 | 501 | 0.72 | 0.81 | 65 | empty |
| 3 | 59 | 0.50 | 0.86 | 14 | SO4 |
| 4 | 57 | 0.47 | 0.85 | 14 | SO4 |
| 5 | 112 | 0.36 | 0.73 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1338 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 1240 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 20 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4ZCV · Structure of calcium-bound regulatory domain of the human ATP-MG/PI carrier in the… · the same entry in another collection · chain D against D, TM-score 1.00
- Q6NUK1 · AlphaFold monomer V2.0 prediction for calcium-binding mitochondrial carrier protein… · a predicted model of the same protein · chain A against A, TM-score 0.92
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 Q6NUK1
- Elsewhere: RCSB PDB 4ZCV · PDBe 4ZCV · UniProt Q6NUK1
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