Research workbench
Structure of the (sr) CA2+-ATPase bound to the inhibitor compound CAD204520 and tnp-ATP
Analyse Structure of the (sr) CA2+-ATPase bound to the inhibitor compound CAD204520 and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YAA
- Type
- protein
- Length
- 994 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SARCOPLASMIC/ENDOPLASMIC reticulum calcium ATPase 1
- EC
- 7.2.2.10
- UniProt
- P04191
- Ligands
- 128, OHW, K
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SARCOPLASMIC/ENDOPLASMIC reticulum calcium ATPase 1 (EC 7.2.2.10) | protein | 994 | 44% helix, 15% strand | P04191 |
Ligands and binding sites
- 128 · Spiro(2,4,6-trinitrobenzene[1,2a]-2O',3O'-methylene-adenine-triphosphate · ligand · chains A
- OHW · 4-[2-[(2~{R})-2-[3-propyl-6-(trifluoromethyloxy)-1~{H}-indol-2-yl]piperidin-1-yl]ethyl]morpholine · ligand · chains A
- K · Potassium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1177 | 0.82 | 0.83 | 87 | 128 |
| 2 | 1139 | 0.74 | 0.77 | 82 | OHW |
| 3 | 501 | 0.71 | 0.80 | 64 | empty |
| 4 | 275 | 0.70 | 0.84 | 35 | empty |
| 5 | 253 | 0.58 | 0.79 | 36 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6YAA · Structure of the (SR) Ca2+-ATPase bound to the inhibitor compound CAD204520 and TNP-ATP · 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 0.96
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 6YAA · PDBe 6YAA · UniProt P04191
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