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Crystal structure of cdp-diacylglycerol pyrophosphatase

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

PDB: 2POF
Type: protein
Length: 440 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cdp-diacylglycerol pyrophosphatase
EC: 3.6.1.26
UniProt: Q8X7A5
Pockets: 4 · best druggability 0.62

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cdp-diacylglycerol pyrophosphatase (EC 3.6.1.26)	protein	220	33% helix, 24% strand	Q8X7A5

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	433	0.62	0.76	44	empty
2	112	0.38	0.75	21	empty
3	57	0.29	0.75	16	empty
4	60	0.27	0.73	17	empty

Interfaces

1 interface between chains.

A–B · 488 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified, 4 disulfide (engineered, disulfide).

Compared structures

2POF · Crystal structure of CDP-diacylglycerol pyrophosphatase · the same entry in another collection · chain A against A, TM-score 1.00
Q8X7A5 · AlphaFold monomer V2.0 prediction for cdp-diacylglycerol pyrophosphatase (Q8X7A5) · a predicted model of the same protein · 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 Q8X7A5
Elsewhere: RCSB PDB 2POF · PDBe 2POF · UniProt Q8X7A5

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