MolNFT v1 · #110966 · protein
Crystal structure of the calcium pump with bound marine macrolide bls
4YCM · SARCOPLASMIC/ENDOPLASMIC reticulum calcium ATPase 1: “Crystal structure of the calcium pump with bound marine macrolide bls”. X-ray diffraction, 4 ligands (PTY, 7BS, NA), 8 pockets (best druggability 0.80). MolNFT v1 #110966 on…
- PDB
- 4YCM
- 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, 7BS, NA, SO4
- Pockets
- 8 · best druggability 0.80
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
- 7BS · (4S,5E,8S,9E,11S,13E,15E,18R)-8-methoxy-9,11-dimethyl-18-[(1Z,4E)-2-methylhexa-1,4-dien-1-yl]-2-oxooxacyclooctadeca-5,9,13,15-tetraen-4-yl 3-O-methyl-beta-D-glucopyranoside · 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
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.80 | 0.82 | 100 | SO4 |
| 2 | 1193 | 0.79 | 0.80 | 87 | 7BS |
| 3 | 816 | 0.75 | 0.79 | 69 | empty |
| 4 | 279 | 0.60 | 0.79 | 39 | empty |
| 5 | 254 | 0.60 | 0.79 | 23 | empty |
Modifications
Observed in the structure: 1 disulfide, 1 modified (disulfide, nonstandard).
Compared structures
- 4YCM · Crystal structure of the calcium pump with bound marine macrolide BLS · 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 4YCM · PDBe 4YCM · UniProt P04191
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