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Crystal structure of pneumococcal lica in complex with choline

Analyse Crystal structure of pneumococcal lica in complex with choline in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4R7B
Type: protein
Length: 573 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Choline kinase
EC: 2.7.1.32
UniProt: Q93MI3
Ligands: CHT
Pockets: 9 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 50% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Choline kinase (EC 2.7.1.32)	protein	287	50% helix, 16% strand	Q93MI3
B	Choline kinase (EC 2.7.1.32)	protein	286	50% helix, 16% strand	Q93MI3

Ligands and binding sites

CHT · Choline ion · ligand · 2 copies · chains A, B

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

Pockets

9 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	363	0.71	0.82	38	CHT
2	372	0.67	0.80	37	CHT
3	506	0.62	0.75	51	empty
4	217	0.60	0.81	39	empty
5	93	0.51	0.83	22	empty

Interfaces

1 interface between chains.

A–B · 505 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

4R7B · Crystal structure of pneumococcal LicA in complex with choline · 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 Q93MI3
Elsewhere: RCSB PDB 4R7B · PDBe 4R7B · UniProt Q93MI3

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