MolNFT v1 · #185209 · protein

C-reactive protein pentamer at pH 7.5 with phosphocholine ligand

7PKE: “C-reactive protein pentamer at pH 7.5 with phosphocholine ligand”. Electron microscopy, 2 ligands (PC, CA), 10 pockets (best druggability 0.64). MolNFT v1 #185209 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7PKE
Type: protein
Length: 1,030 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: C-reactive protein
UniProt: P02741
Ligands: PC, CA
Pockets: 10 · best druggability 0.64

Structure

electron microscopy · 1 distinct chain · 8% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E, D, C, B, A	C-reactive protein	protein	206	8% helix, 46% strand	P02741

Ligands and binding sites

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

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	549	0.64	0.76	79	empty
2	529	0.63	0.75	78	empty
3	333	0.59	0.77	53	empty
4	163	0.48	0.77	28	empty
5	159	0.46	0.76	29	empty

Interfaces

5 interfaces between chains.

E–A · 707 Å² buried · 8 hydrogen bonds · protein-protein
E–D · 707 Å² buried · 6 hydrogen bonds · protein-protein
D–C · 698 Å² buried · 9 hydrogen bonds · protein-protein
B–A · 683 Å² buried · 8 hydrogen bonds · protein-protein
C–B · 670 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

7PKE · C-reactive protein pentamer at pH 7.5 with phosphocholine ligand · 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 E 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 7PKE · PDBe 7PKE · UniProt P02741

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