MolNFT v1 · #60915 · protein

Crystal structure of inorganic pyrophosphatase from burkholderia pseudomallei

3D63: “Crystal structure of inorganic pyrophosphatase from burkholderia pseudomallei”. X-ray diffraction, 5 pockets (best druggability 0.80). MolNFT v1 #60915 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3D63
Type: protein
Length: 524 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Inorganic pyrophosphatase
EC: 3.6.1.1
UniProt: Q3JUV5
Pockets: 5 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 17% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Inorganic pyrophosphatase (EC 3.6.1.1)	protein	173	18% helix, 35% strand	Q3JUV5
C	Inorganic pyrophosphatase (EC 3.6.1.1)	protein	178	17% helix, 37% strand	Q3JUV5

Pockets

5 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	1166	0.80	0.82	117	empty
2	123	0.52	0.80	20	empty
3	143	0.51	0.79	22	empty
4	218	0.48	0.74	32	empty
5	53	0.27	0.74	19	empty

Interfaces

3 interfaces between chains.

B–C · 278 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 230 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 195 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

3D63 · Crystal structure of inorganic pyrophosphatase from Burkholderia pseudomallei · 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
Every structure of UniProt Q3JUV5
Elsewhere: RCSB PDB 3D63 · PDBe 3D63 · UniProt Q3JUV5

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