MolNFT v1 · #142502 · protein
Cryo-EM structure of a P-type ATPase
6A69 · Plasma membrane calcium-transporting ATPase 1: “Cryo-EM structure of a P-type ATPase”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.76). MolNFT v1 #142502 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6A69
- Type
- protein
- Length
- 1,038 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasma membrane calcium-transporting ATPase 1; Neuroplastin
- EC
- 3.6.3.8
- UniProt
- P20020, Q9Y639
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 2 distinct chains · 39% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plasma membrane calcium-transporting ATPase 1 (EC 3.6.3.8) | protein | 911 | 42% helix, 8% strand | P20020 |
| B | Neuroplastin | protein | 127 | 16% helix, 44% strand | Q9Y639 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 642 | 0.76 | 0.82 | 78 | empty |
| 2 | 243 | 0.69 | 0.85 | 37 | empty |
| 3 | 369 | 0.66 | 0.80 | 49 | empty |
| 4 | 432 | 0.66 | 0.79 | 44 | empty |
| 5 | 208 | 0.66 | 0.84 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 894 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6A69 · Cryo-EM structure of a P-type ATPase · the same entry in another collection · chain A against A, TM-score 1.00
- P20020 · AlphaFold monomer V2.0 prediction for plasma membrane calcium- transporting ATPase 1… · a predicted model of the same protein · chain A against A, TM-score 0.95
- Q9Y639 · AlphaFold monomer V2.0 prediction for neuroplastin (Q9Y639) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 P20020
- Every structure of UniProt Q9Y639
- Elsewhere: RCSB PDB 6A69 · PDBe 6A69 · UniProt P20020 · UniProt Q9Y639
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