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Structure of inorganic pyrophosphatase

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

PDB: 1OBW
Type: protein
Length: 525 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Inorganic pyrophosphatase
EC: 3.6.1.1
UniProt: P0A7A9
Ligands: MG
Pockets: 6 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 21% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Inorganic pyrophosphatase (EC 3.6.1.1)	protein	175	21% helix, 33% strand	P0A7A9

Ligands and binding sites

MG · Magnesium ion · metal · 7 copies · chains A, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	411	0.83	0.91	33	empty
2	294	0.64	0.81	38	MG
3	227	0.62	0.82	36	MG
4	295	0.62	0.79	36	empty
5	349	0.58	0.76	36	empty

Interfaces

3 interfaces between chains.

A–B · 777 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 755 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 750 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

1OBW · 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 1OBW · PDBe 1OBW · UniProt P0A7A9

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