MolNFT v1 · #185208 · protein

C-reactive protein decamer at pH 7.5 with phosphocholine ligand

7PKD: “C-reactive protein decamer at pH 7.5 with phosphocholine ligand”. Electron microscopy, 2 ligands (PC, CA), 20 pockets (best druggability 0.82). MolNFT v1 #185208 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7PKD
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: PC, CA
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 1 distinct chain · 9% helix, 45% 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, 45% strand	P02741

Ligands and binding sites

PC · Phosphocholine · ligand · 10 copies · chains J, F, G, H, I, E, D, C, B, A
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, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	954	0.82	0.84	116	empty
2	1045	0.78	0.80	127	empty
3	245	0.71	0.86	34	empty
4	305	0.63	0.79	56	empty
5	402	0.61	0.77	61	empty

Interfaces

16 interfaces between chains.

C–B · 745 Å² buried · 9 hydrogen bonds · protein-protein
F–G · 728 Å² buried · 10 hydrogen bonds · protein-protein
E–D · 728 Å² buried · 10 hydrogen bonds · protein-protein
E–A · 722 Å² buried · 6 hydrogen bonds · protein-protein
G–H · 711 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

7PKD · C-reactive protein decamer 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 F 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 7PKD · PDBe 7PKD · UniProt P02741

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