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Structure of inorganic pyrophosphatase crystallised as a contaminant

Analyse Structure of inorganic pyrophosphatase crystallised as a contaminant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5H4F
Type: protein
Length: 347 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Inorganic pyrophosphatase
EC: 3.6.1.1
Ligands: ZN
Pockets: 6 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains · 18% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Inorganic pyrophosphatase (EC 3.6.1.1)	protein	175	18% helix, 34% strand	—
B	Inorganic pyrophosphatase (EC 3.6.1.1)	protein	172	17% helix, 35% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B

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

Pockets

6 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	260	0.62	0.80	39	empty
2	193	0.54	0.79	37	empty
3	135	0.40	0.74	28	empty
4	117	0.39	0.74	28	empty
5	63	0.38	0.79	17	empty

Interfaces

1 interface between chains.

A–B · 705 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5H4F · Structure of inorganic pyrophosphatase crystallised as a contaminant · the same entry in another collection · 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
Elsewhere: RCSB PDB 5H4F · PDBe 5H4F

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