Research workbench
Crystal structure of the sr CA2+-ATPase with bhq and tg
Analyse Crystal structure of the sr CA2+-ATPase with bhq and tg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AGV
- Type
- protein
- Length
- 1,988 residues
- Chains
- 2
- 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
- PTY, TG1, BHQ, NA
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | SARCOPLASMIC/ENDOPLASMIC reticulum calcium ATPase 1 (EC 3.6.3.8) | protein | 994 | 47% helix, 17% strand | P04191 |
Ligands and binding sites
- PTY · Phosphatidylethanolamine · ligand · 6 copies · chains A, B
- 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 · 2 copies · chains A, B
- BHQ · 2,5-ditert-butylbenzene-1,4-diol · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 781 | 0.80 | 0.84 | 91 | empty |
| 2 | 1191 | 0.80 | 0.82 | 108 | empty |
| 3 | 1103 | 0.77 | 0.79 | 81 | empty |
| 4 | 980 | 0.76 | 0.79 | 70 | empty |
| 5 | 984 | 0.73 | 0.76 | 85 | BHQ, PTY |
Interfaces
1 interface between chains.
- A–B · 532 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2AGV · Crystal structure of the SR CA2+-ATPASE with BHQ and TG · 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 0.95
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 2AGV · PDBe 2AGV · UniProt P04191
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