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Crystal structure of the choline binding domain of SPR1274 in streptococcus pneumoniae

Analyse Crystal structure of the choline binding domain of SPR1274 in streptococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3HIA
Type: protein
Length: 223 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Choline binding protein
UniProt: Q8DP99
Ligands: PC, SO4
Pockets: 3 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 0% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Choline binding protein	protein	66	0% helix, 50% strand	Q8DP99
B	Choline binding protein	protein	83	0% helix, 51% strand	Q8DP99
C	Choline binding protein	protein	74	0% helix, 45% strand	Q8DP99

Ligands and binding sites

PC · Phosphocholine · ligand · 7 copies · chains A, B, C
SO4 · Sulfate ion · ion · 3 copies · chains A, B, C

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	354	0.69	0.82	43	PC, SO4
2	249	0.62	0.81	30	PC
3	83	0.38	0.77	12	PC

Interfaces

3 interfaces between chains.

A–B · 653 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 404 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 370 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

3HIA · Crystal structure of the choline binding domain of Spr1274 in Streptococcus pneumoniae · the same entry in another collection · chain A against A, TM-score 1.00

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Every structure of UniProt Q8DP99
Elsewhere: RCSB PDB 3HIA · PDBe 3HIA · UniProt Q8DP99

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