Research workbench
Structure of P5A-ATPase Spf1, endogenous substrate-bound
Analyse Structure of P5A-ATPase Spf1, endogenous substrate-bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XMU
- Type
- protein
- Length
- 1,110 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.3
- Source
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Molecule
- P5A-type ATPase; Putative endogenous substrate transmembrane helix
- EC
- 7.2.2.-
- UniProt
- P39986
- Ligands
- BEF, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · resolution 3.3 · 2 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | P5A-type ATPase (EC 7.2.2.-) | protein | 1090 | 40% helix, 16% strand | P39986 |
| B | Putative endogenous substrate transmembrane helix | protein | 20 | 90% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1043 | 0.83 | 0.83 | 105 | empty |
| 2 | 564 | 0.73 | 0.81 | 65 | empty |
| 3 | 434 | 0.72 | 0.82 | 37 | empty |
| 4 | 171 | 0.66 | 0.86 | 26 | empty |
| 5 | 497 | 0.65 | 0.77 | 60 | empty |
Interfaces
1 interface between chains.
- A–B · 344 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6XMU · Structure of P5A-ATPase SPF1, endogenous substrate-bound · the same entry in another collection · chain A against A, TM-score 1.00
- P39986 · AlphaFold monomer V2.0 prediction for endoplasmic reticulum transmembrane helix… · a predicted model of the same protein · chain A against A, TM-score 0.79
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 P39986
- Elsewhere: RCSB PDB 6XMU · PDBe 6XMU · UniProt P39986
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