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Crystal structure of the (sr) calcium ATPase E2-vanadate complex bound to thapsigargin and tnp-amppcp
Analyse Crystal structure of the (sr) calcium ATPase E2-vanadate complex bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A3Q
- Type
- protein
- Length
- 993 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
- ACE, TG1, VN4, DL5, MG, K, CL
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SARCOPLASMIC/ENDOPLASMIC reticulum calcium ATPase 1 (EC 3.6.3.8) | protein | 993 | 48% helix, 17% strand | P04191 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A
- TG1 · Octanoic acid [3S-[3alpha, 3abeta, 4alpha, 6beta, 6abeta, 7beta, 8alpha(z), 9balpha]]-6-(acetyloxy)-2,3, -3A,4,5,6,6A,7,8,9B-decahydro-3,3A-dihydroxy-3,6,9-trimethyl-8-[(2-methyl-1-oxo-2-butenyl)oxy]-2-oxo-4-(1-oxobutoxy)-azuleno[4,5-b]furan-7-yl ester · ligand · chains A
- VN4 · oxido(dioxo)vanadium · ligand · chains A
- DL5 · Spiro(2,4,6-trinitrobenzene[1,2a]-O2',O3'-methylene-adenosine (beta,gamma-methylene)triphosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- K · Potassium ion · metal · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1133 | 0.78 | 0.80 | 81 | empty |
| 2 | 927 | 0.76 | 0.79 | 62 | empty |
| 3 | 673 | 0.75 | 0.81 | 60 | DL5, MG |
| 4 | 295 | 0.60 | 0.78 | 28 | TG1 |
| 5 | 236 | 0.55 | 0.78 | 30 | empty |
Modifications
Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 5A3Q · Crystal structure of the (SR) Calcium ATPase E2-vanadate complex bound to thapsigargin… · 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 0.93
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 5A3Q · PDBe 5A3Q · UniProt P04191
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