Research workbench
Crystal structure of the sr CA2+-ATPase with MGF4
Analyse Crystal structure of the sr CA2+-ATPase with MGF4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WPG
- Type
- protein
- Length
- 3,976 residues
- Chains
- 4
- 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
- MF4, ADP, TG1, MG, NA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | SARCOPLASMIC/ENDOPLASMIC reticulum calcium ATPase 1 (EC 3.6.3.8) | protein | 994 | 47% helix, 16% strand | P04191 |
Ligands and binding sites
- MF4 · Tetrafluoromagnesate(2-) · ligand · 4 copies · chains A, B, C, D
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- 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 · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.84 | 0.85 | 96 | TG1 |
| 2 | 1050 | 0.81 | 0.83 | 75 | empty |
| 3 | 1102 | 0.79 | 0.80 | 79 | empty |
| 4 | 1080 | 0.79 | 0.80 | 81 | empty |
| 5 | 852 | 0.76 | 0.80 | 68 | empty |
Interfaces
4 interfaces between chains.
- C–D · 403 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 400 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 129 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 39 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1WPG · Crystal structure of the SR CA2+-ATPase with MGF4 · the same entry in another collection · chain D against D, 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 0.92
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 1WPG · PDBe 1WPG · UniProt P04191
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