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Crystal structure of calcium ATPase with bound magnesium fluoride and cyclopiazonic acid
Analyse Crystal structure of calcium ATPase with bound magnesium fluoride and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2O9J
- Type
- protein
- Length
- 980 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SARCOPLASMIC/ENDOPLASMIC reticulum calcium ATPase 1
- EC
- 3.6.3.8
- UniProt
- P04191
- Ligands
- MF4, CZA, MG, NA
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SARCOPLASMIC/ENDOPLASMIC reticulum calcium ATPase 1 (EC 3.6.3.8) | protein | 980 | 45% helix, 17% strand | P04191 |
Ligands and binding sites
- MF4 · Tetrafluoromagnesate(2-) · ligand · chains A
- CZA · (6ar,11as,11br)-10-acetyl-9-hydroxy-7,7-dimethyl-2,6, 6A,7,11A,11B-hexahydro-11H-pyrrolo[1',2':2, 3]isoindolo[4,5,6-cd]indol-11-one · ligand · chains A
- MG · Magnesium ion · metal · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1144 | 0.84 | 0.85 | 80 | NA, CZA |
| 2 | 866 | 0.74 | 0.78 | 88 | empty |
| 3 | 468 | 0.68 | 0.79 | 41 | empty |
| 4 | 162 | 0.62 | 0.84 | 20 | empty |
| 5 | 267 | 0.60 | 0.79 | 32 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2O9J · Crystal structure of calcium atpase with bound magnesium fluoride and cyclopiazonic acid · the same entry in another collection · chain A against A, TM-score 1.00
- P04191 · AlphaFold monomer V2.0 prediction for SARCOPLASMIC/ENDOPLASMIC reticulum calcium ATPase 1… · 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 P04191
- Elsewhere: RCSB PDB 2O9J · PDBe 2O9J · UniProt P04191
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