MolNFT v1 · #21439 · protein

The structure of pentameric human serum amyloid P component

1SAC: “The structure of pentameric human serum amyloid P component”. X-ray diffraction, 1 ligand (CA), 4 pockets (best druggability 0.31). MolNFT v1 #21439 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1SAC
Type: protein
Length: 1,020 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Serum amyloid P component
UniProt: P02743
Ligands: CA
Pockets: 4 · best druggability 0.31

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Serum amyloid P component	protein	204	5% helix, 46% strand	P02743

Ligands and binding sites

CA · Calcium ion · metal · 10 copies · chains A, B, C, D, E
ACY · Acetic acid · additive · 4 copies · chains A, B, D, E

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

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	71	0.31	0.74	14	empty
2	77	0.30	0.73	19	empty
3	62	0.29	0.74	16	empty
4	55	0.27	0.73	15	empty

Interfaces

5 interfaces between chains.

A–E · 767 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 764 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 763 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 759 Å² buried · 10 hydrogen bonds · protein-protein
D–E · 757 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

1SAC · The structure of pentameric human serum amyloid P component · the same entry in another collection · chain A against A, 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 1SAC · PDBe 1SAC · UniProt P02743

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