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Crystal structure of the calcium pump with bound marine macrolide bllb
Analyse Crystal structure of the calcium pump with bound marine macrolide bllb in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YCN
- 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
- PTY, 7BL, NA, SO4
- Pockets
- 9 · best druggability 0.83
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
- PTY · Phosphatidylethanolamine · ligand · 2 copies · chains A
- 7BL · (4S,5E,8S,9E,11S,13E,15E,18R)-4-hydroxy-8-methoxy-9,11-dimethyl-18-[(1Z,4E)-2-methylhexa-1,4-dien-1-yl]oxacyclooctadeca-5,9,13,15-tetraen-2-one · ligand · chains A
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1049 | 0.83 | 0.84 | 89 | 7BL |
| 2 | 1088 | 0.80 | 0.82 | 93 | SO4 |
| 3 | 799 | 0.72 | 0.77 | 76 | empty |
| 4 | 216 | 0.58 | 0.80 | 33 | empty |
| 5 | 215 | 0.54 | 0.78 | 25 | empty |
Modifications
Observed in the structure: 1 disulfide, 1 modified (disulfide, nonstandard).
Compared structures
- 4YCN · Crystal structure of the calcium pump with bound marine macrolide BLLB · 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 0.97
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 4YCN · PDBe 4YCN · UniProt P04191
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