MolNFT v1 · #113050 · protein
Crystal structure of the (sr) calcium ATPase E2.BEF3- complex bound to tnp-amppcp
5A3R · SARCOPLASMIC/ENDOPLASMIC reticulum calcium ATPase 1: “Crystal structure of the (sr) calcium ATPase E2.BEF3- complex bound to tnp-amppcp”. X-ray diffraction, 3 ligands (DL5, MG, K), 11 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 5A3R
- 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
- 3.6.3.8
- UniProt
- P04191
- Ligands
- DL5, MG, K
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SARCOPLASMIC/ENDOPLASMIC reticulum calcium ATPase 1 (EC 3.6.3.8) | protein | 994 | 46% helix, 16% strand | P04191 |
Ligands and binding sites
- DL5 · Spiro(2,4,6-trinitrobenzene[1,2a]-O2',O3'-methylene-adenosine (beta,gamma-methylene)triphosphate · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A
- K · Potassium 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.80 | 0.82 | 103 | empty |
| 2 | 143 | 0.77 | 0.94 | 26 | empty |
| 3 | 426 | 0.64 | 0.78 | 57 | DL5 |
| 4 | 376 | 0.63 | 0.78 | 40 | MG |
| 5 | 230 | 0.56 | 0.78 | 32 | empty |
Modifications
Observed in the structure: 1 disulfide, 1 modified (disulfide, nonstandard).
Compared structures
- 5A3R · Crystal structure of the (SR) Calcium ATPase E2.BeF3- complex bound to TNP-AMPPCP · 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 0.85
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 5A3R · PDBe 5A3R · UniProt P04191
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