Research workbench
Sr CA(2+)-ATPase in the HNE2 state complexed with the thapsigargin derivative boc-12ADT.
Analyse Sr CA(2+)-ATPase in the HNE2 state complexed with the thapsigargin derivative… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BY4
- 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
- AD4, ACP, MG, NA
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SARCOPLASMIC/ENDOPLASMIC reticulum calcium ATPase 1 (EC 3.6.3.8) | protein | 994 | 45% helix, 15% strand | P04191 |
Ligands and binding sites
- AD4 · (3s,3ar,4s,6s,6ar,7s,8s,9bs)-6-(acetyloxy)-3, 3A-dihydroxy-3,6,9-trimethyl-8-{[(2Z)-2-methylbut-2-enoyl]oxy}-7-(octanoyloxy)-2-oxo-2,3, 3A,4,5,6,6A,7,8,9B-decahydroazuleno[4,5-B] furan-4-yl 12-[(tert-butoxycarbonyl)amino] dodecanoate · ligand · chains A
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1142 | 0.80 | 0.82 | 101 | ACP, MG |
| 2 | 936 | 0.77 | 0.79 | 72 | empty |
| 3 | 805 | 0.76 | 0.80 | 68 | AD4 |
| 4 | 328 | 0.61 | 0.79 | 37 | NA |
| 5 | 276 | 0.60 | 0.79 | 34 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2BY4 · SR Ca(2+)-ATPase in the HnE2 state complexed with the thapsigargin derivative Boc-12ADT. · 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 2BY4 · PDBe 2BY4 · UniProt P04191
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