MolNFT v1 · #5160 · protein

Structure of inorganic pyrophosphatase

1E9G: “Structure of inorganic pyrophosphatase”. X-ray diffraction, 2 ligands (MN, PO4), 5 pockets (best druggability 0.64). MolNFT v1 #5160 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1E9G
Type: protein
Length: 567 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Inorganic pyrophosphatase
EC: 3.6.1.1
UniProt: P00817
Ligands: MN, PO4
Pockets: 5 · best druggability 0.64

Structure

x-ray diffraction · 2 distinct chains · 19% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Inorganic pyrophosphatase (EC 3.6.1.1)	protein	284	19% helix, 30% strand	P00817
B	Inorganic pyrophosphatase (EC 3.6.1.1)	protein	283	19% helix, 31% strand	P00817

Ligands and binding sites

MN · Manganese (II) ion · metal · 8 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

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	566	0.64	0.75	43	empty
2	154	0.52	0.80	26	MN, PO4
3	153	0.50	0.79	31	MN, PO4
4	61	0.47	0.84	19	empty
5	69	0.30	0.73	15	empty

Interfaces

1 interface between chains.

A–B · 1029 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

1E9G · Structure of inorganic pyrophosphatase · the same entry in another collection · chain A against A, TM-score 1.00
P00817 · AlphaFold monomer V2.0 prediction for inorganic pyrophosphatase (P00817) · 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 P00817
Elsewhere: RCSB PDB 1E9G · PDBe 1E9G · UniProt P00817

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