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Crystal structure of choline binding protein F from streptococcus pneumoniae in the presence of a peptidoglycan analogue (tetrasaccharide-pentapeptide)

Analyse Crystal structure of choline binding protein F from streptococcus pneumoniae in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2VYU
Type: protein
Length: 300 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Choline binding protein F
UniProt: Q8DR52
Ligands: CHT
Pockets: 3 · best druggability 0.38

Structure

x-ray diffraction · 1 distinct chain · 1% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Choline binding protein F	protein	300	1% helix, 45% strand	Q8DR52

Ligands and binding sites

CHT · Choline ion · ligand · 7 copies · chains A

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	64	0.38	0.79	20	empty
2	52	0.30	0.75	16	empty
3	79	0.28	0.71	20	empty

Compared structures

2VYU · Crystal structure of choline binding protein F from streptococcus pneumoniae in the… · 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 Q8DR52
Elsewhere: RCSB PDB 2VYU · PDBe 2VYU · UniProt Q8DR52

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