Research workbench

Human C-reactive protein complexed with phosphocholine

Analyse Human C-reactive protein complexed with phosphocholine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1B09
Type: protein
Length: 1,030 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (C-reactive protein)
UniProt: P02741
Ligands: PC, CA
Pockets: 14 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 9% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Protein (C-reactive protein)	protein	206	9% helix, 42% strand	P02741

Ligands and binding sites

PC · Phosphocholine · ligand · 5 copies · chains A, B, C, D, E
CA · Calcium ion · metal · 10 copies · chains A, B, C, D, E

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

Pockets

14 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	294	0.59	0.78	49	empty
2	183	0.53	0.78	24	empty
3	158	0.53	0.80	25	empty
4	143	0.52	0.80	23	empty
5	179	0.51	0.77	28	empty

Interfaces

5 interfaces between chains.

A–B · 703 Å² buried · 8 hydrogen bonds · protein-protein
D–E · 687 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 658 Å² buried · 7 hydrogen bonds · protein-protein
A–E · 654 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 643 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

1B09 · Human C-reactive protein complexed with phosphocholine · the same entry in another collection · chain C against C, TM-score 1.00
P02741 · AlphaFold monomer V2.0 prediction for C-reactive protein (P02741) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P02741
Elsewhere: RCSB PDB 1B09 · PDBe 1B09 · UniProt P02741

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