Research workbench
Serca in the HNE2 state complexed with debutanoyl thapsigargin
Analyse Serca in the HNE2 state complexed with debutanoyl thapsigargin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YFY
- 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
- 9TN, K, MG
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SARCOPLASMIC/ENDOPLASMIC reticulum calcium ATPase 1 (EC 3.6.3.8) | protein | 994 | 49% helix, 17% strand | P04191 |
Ligands and binding sites
- 9TN · Debutanoyl thapsigargin · ligand · chains A
- K · Potassium ion · metal · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1055 | 0.79 | 0.81 | 98 | MG |
| 2 | 814 | 0.77 | 0.80 | 68 | 9TN |
| 3 | 510 | 0.70 | 0.80 | 52 | empty |
| 4 | 307 | 0.60 | 0.78 | 39 | K |
| 5 | 82 | 0.55 | 0.86 | 21 | empty |
Modifications
Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 2YFY · SERCA in the HnE2 State Complexed With Debutanoyl Thapsigargin · 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 0.95
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 2YFY · PDBe 2YFY · UniProt P04191
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