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Proton pyrophosphatase-E225H mutant

Analyse Proton pyrophosphatase-E225H mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6AFZ
Type: protein
Length: 1,480 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.483
Source: Vigna radiata var. radiata
Molecule: Pyrophosphate-energized vacuolar membrane proton pump
EC: 3.6.1.1
UniProt: P21616
Ligands: 1PG, MG, K, PO4
Pockets: 17 · best druggability 0.78

Structure

x-ray diffraction · resolution 2.483 · 1 distinct chain · 82% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Pyrophosphate-energized vacuolar membrane proton pump (EC 3.6.1.1)	protein	740	82% helix, 3% strand	P21616

Ligands and binding sites

1PG · 2-(2-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethanol · ligand · 7 copies · chains A, B
MG · Magnesium ion · metal · 10 copies · chains A, B
K · Potassium ion · metal · 2 copies · chains A, B
PO4 · Phosphate ion · ion · 4 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	112	0.78	0.98	30	PO4, MG, K
2	120	0.76	0.96	29	PO4, MG, K
3	79	0.75	0.98	24	empty
4	260	0.70	0.85	42	empty
5	51	0.70	0.98	21	empty

Interfaces

1 interface between chains.

A–B · 3300 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

6AFZ · Proton pyrophosphatase-E225H mutant · the same entry in another collection · chain A against A, TM-score 1.00
P21616 · AlphaFold monomer V2.0 prediction for pyrophosphate-energized vacuolar membrane proton… · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P21616
Elsewhere: RCSB PDB 6AFZ · PDBe 6AFZ · UniProt P21616

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