MolNFT v1 · #98089 · protein
The structure of superinhibitory phospholamban bound to the calcium pump SERCA1A
4KYT: “The structure of superinhibitory phospholamban bound to the calcium pump SERCA1A”. X-ray diffraction, 2 ligands (GLC, K), 14 pockets (best druggability 0.76). MolNFT v1 #98089 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4KYT
- Type
- protein
- Length
- 1,019 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERCA1A; Cardiac phospholamban
- UniProt
- B6CAM1, P61012
- Ligands
- GLC, K
- Pockets
- 14 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERCA1A | protein | 975 | 46% helix, 17% strand | B6CAM1 |
| B | Cardiac phospholamban | protein | 29 | 79% helix, 0% strand | P61012 |
| C | Cardiac phospholamban | protein | 15 | 47% helix, 0% strand | P61012 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.76 | 0.86 | 38 | empty |
| 2 | 453 | 0.70 | 0.81 | 51 | empty |
| 3 | 289 | 0.70 | 0.84 | 37 | empty |
| 4 | 692 | 0.68 | 0.76 | 52 | empty |
| 5 | 419 | 0.65 | 0.79 | 45 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1181 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 441 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 49 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4KYT · The structure of superinhibitory phospholamban bound to the calcium pump SERCA1a · the same entry in another collection · chain A against A, TM-score 1.00
- P61012 · AlphaFold monomer V2.0 prediction for cardiac phospholamban (P61012) · a predicted model of the same protein · chain B against A, TM-score 0.73
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 B6CAM1
- Every structure of UniProt P61012
- Elsewhere: RCSB PDB 4KYT · PDBe 4KYT · UniProt B6CAM1 · UniProt P61012
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