MolNFT v1 · #11195 · protein

Structure of inorganic pyrophosphatase

1JFD: “Structure of inorganic pyrophosphatase”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.72). MolNFT v1 #11195 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1JFD
Type: protein
Length: 350 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Inorganic pyrophosphatase
EC: 3.6.1.1
UniProt: P0A7A9
Ligands: SO4
Pockets: 4 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 20% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Inorganic pyrophosphatase (EC 3.6.1.1)	protein	175	20% helix, 33% strand	P0A7A9

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	796	0.72	0.77	51	empty
2	219	0.57	0.79	34	SO4
3	184	0.50	0.77	29	SO4
4	70	0.39	0.79	17	empty

Interfaces

1 interface between chains.

A–B · 188 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

1JFD · Structure of inorganic pyrophosphatase · the same entry in another collection · chain A against A, TM-score 1.00
P0A7A9 · AlphaFold monomer V2.0 prediction for inorganic pyrophosphatase (P0A7A9) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P0A7A9
Elsewhere: RCSB PDB 1JFD · PDBe 1JFD · UniProt P0A7A9

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