Research workbench

C-reactive protein decamer at pH 5

Analyse C-reactive protein decamer at pH 5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7PKF
Type: protein
Length: 2,060 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: C-reactive protein
UniProt: P02741
Ligands: CA
Pockets: 20 · best druggability 0.80

Structure

electron microscopy · 1 distinct chain · 9% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
J, F, G, H, I, E, D, C, B, A	C-reactive protein	protein	206	9% helix, 44% strand	P02741

Ligands and binding sites

CA · Calcium ion · metal · 20 copies · chains J, F, G, H, I, E, D, C, B, A

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

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	842	0.80	0.83	68	empty
2	722	0.79	0.83	98	empty
3	471	0.78	0.86	60	empty
4	188	0.60	0.82	27	empty
5	210	0.58	0.80	50	empty

Interfaces

16 interfaces between chains.

G–H · 752 Å² buried · 11 hydrogen bonds · protein-protein
J–F · 733 Å² buried · 11 hydrogen bonds · protein-protein
C–B · 722 Å² buried · 11 hydrogen bonds · protein-protein
E–A · 704 Å² buried · 9 hydrogen bonds · protein-protein
J–I · 698 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

7PKF · C-reactive protein decamer at pH 5 · the same entry in another collection · chain A against A, 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 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 P02741
Elsewhere: RCSB PDB 7PKF · PDBe 7PKF · UniProt P02741

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