Research workbench
Crystal structure of the sr calcium pump with bound aluminium fluoride, ADP and calcium
Analyse Crystal structure of the sr calcium pump with bound aluminium fluoride, ADP and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZBD
- 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
- PC1, ACE, ALF, ADP, CA, MG
- Pockets
- 17 · best druggability 0.85
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
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 2 copies · chains A
- ACE · Acetyl group · ligand · chains A
- ALF · Tetrafluoroaluminate ion · ligand · chains A
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- CA · Calcium ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 910 | 0.85 | 0.87 | 103 | MG, ALF, ADP |
| 2 | 512 | 0.71 | 0.80 | 39 | empty |
| 3 | 271 | 0.65 | 0.82 | 39 | empty |
| 4 | 247 | 0.62 | 0.81 | 27 | empty |
| 5 | 307 | 0.59 | 0.78 | 27 | empty |
Modifications
Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 2ZBD · Crystal Structure of the SR Calcium Pump with Bound Aluminium Fluoride, ADP and Calcium · 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 0.69
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 2ZBD · PDBe 2ZBD · UniProt P04191
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