MolNFT v1 · #32380 · protein

Structure of an escherichia COLI lipid kinase (yegs)

2BON: “Structure of an escherichia COLI lipid kinase (yegs)”. X-ray diffraction, 1 ligand (MG), 3 pockets (best druggability 0.56). MolNFT v1 #32380 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2BON
Type: protein
Length: 552 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lipid kinase
UniProt: P76407
Ligands: MG
Pockets: 3 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains · 23% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lipid kinase	protein	287	24% helix, 40% strand	P76407
B	Lipid kinase	protein	265	21% helix, 40% strand	P76407

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

3 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	208	0.56	0.79	29	empty
2	249	0.53	0.76	44	empty
3	214	0.50	0.76	41	empty

Interfaces

1 interface between chains.

A–B · 564 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

2BON · Structure of an Escherichia coli lipid kinase (YegS) · the same entry in another collection · chain A against A, TM-score 1.00
P76407 · AlphaFold monomer V2.0 prediction for lipid kinase yegs (P76407) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 P76407
Elsewhere: RCSB PDB 2BON · PDBe 2BON · UniProt P76407

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