MolNFT v1 · #142798 · protein

Proton pyrophosphatase-L555M mutant

6AFU · Pyrophosphate-energized vacuolar membrane proton pump: “Proton pyrophosphatase-L555M mutant”. X-ray diffraction, 4 ligands (1PG, MG, K), 15 pockets (best druggability 0.77). MolNFT v1 #142798 on GenesisL1: 3D structure, binding…

PDB: 6AFU
Type: protein
Length: 1,480 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyrophosphate-energized vacuolar membrane proton pump
EC: 3.6.1.1
UniProt: P21616
Ligands: 1PG, MG, K, PO4
Pockets: 15 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 82% helix, 2% 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, 2% strand	P21616

Ligands and binding sites

1PG · 2-(2-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethanol · ligand · 4 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

15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	100	0.77	0.99	30	PO4, MG, K
2	123	0.77	0.97	36	PO4, MG, K
3	267	0.73	0.87	44	empty
4	59	0.72	0.98	17	empty
5	338	0.71	0.83	44	empty

Interfaces

1 interface between chains.

A–B · 3319 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

6AFU · Proton pyrophosphatase-L555M 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 B 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 6AFU · PDBe 6AFU · UniProt P21616

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