MolNFT v1 · #86083 · protein

Structure of cphpc bound to serum amyloid P component

4AVT · Serum amyloid P-component: “Structure of cphpc bound to serum amyloid P component”. X-ray diffraction, 3 ligands (GHE, NAG, CA), 20 pockets (best druggability 0.59). MolNFT v1 #86083 on GenesisL1: 3D structure, binding sites and…

PDB: 4AVT
Type: protein
Length: 2,040 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Serum amyloid P-component
UniProt: P02743
Ligands: GHE, NAG, CA
Pockets: 20 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J	Serum amyloid P-component	protein	204	5% helix, 47% strand	P02743

Ligands and binding sites

GHE · (2R)-1-[6-[(2R)-2-carboxypyrrolidin-1-yl]-6-oxidanylidene-hexanoyl]pyrrolidine-2-carboxylic acid · ligand · 5 copies · chains A, B, C, D, E, F, G, H, I, J
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B, C, D, E, F, G, H, I, J
CA · Calcium ion · metal · 20 copies · chains A, B, C, D, E, F, G, H, I, J

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

Pockets

20 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	441	0.59	0.75	44	GHE, CA
2	451	0.59	0.75	32	GHE
3	404	0.58	0.75	30	GHE
4	389	0.55	0.74	30	GHE
5	340	0.52	0.73	31	GHE

Interfaces

15 interfaces between chains.

C–E · 782 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 779 Å² buried · 9 hydrogen bonds · protein-protein
E–G · 776 Å² buried · 9 hydrogen bonds · protein-protein
D–F · 775 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 775 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 glycan (N-glycosylation).

Compared structures

4AVT · Structure of CPHPC bound to Serum Amyloid P Component · the same entry in another collection · chain J against J, TM-score 1.00
P02743 · AlphaFold monomer V2.0 prediction for serum amyloid P-component (P02743) · 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 P02743
Elsewhere: RCSB PDB 4AVT · PDBe 4AVT · UniProt P02743

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