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Dgka structure in E.COLI lipid bilayer

Analyse Dgka structure in E.COLI lipid bilayer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7DVM
Type: protein
Length: 363 residues
Chains: 3
Method: solid-state nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Diacylglycerol kinase
EC: 2.7.1.107
UniProt: A0A0H3MWQ1
Pockets: 6 · best druggability 0.86

Structure

solid-state nmr · 1 distinct chain · 89% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Diacylglycerol kinase (EC 2.7.1.107)	protein	121	89% helix, 0% strand	A0A0H3MWQ1

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	308	0.86	0.96	41	empty
2	70	0.74	0.98	27	empty
3	67	0.39	0.78	15	empty
4	71	0.39	0.78	14	empty
5	63	0.38	0.78	12	empty

Interfaces

3 interfaces between chains.

A–C · 1791 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1789 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 1786 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 modified (nonstandard).

Compared structures

7DVM · DgkA structure in E.coli lipid bilayer · 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 A0A0H3MWQ1
Elsewhere: RCSB PDB 7DVM · PDBe 7DVM · UniProt A0A0H3MWQ1

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