MolNFT v1 · #56315 · protein
Crystal structure of the sr calcium pump with bound aluminium fluoride, ADP and calcium
2ZBD · SARCOPLASMIC/ENDOPLASMIC reticulum calcium ATPase 1: “Crystal structure of the sr calcium pump with bound aluminium fluoride, ADP and calcium”. X-ray diffraction, 6 ligands (PC1, ACE, ALF), 17 pockets (best druggability 0.85).…
- 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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