MolNFT v1 · #13584 · protein

Decameric damp complex of human serum amyloid P component

1LGN: “Decameric damp complex of human serum amyloid P component”. X-ray diffraction, 2 ligands (DA, CA), 8 pockets (best druggability 0.55). MolNFT v1 #13584 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1LGN
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: DA, CA
Pockets: 8 · best druggability 0.55

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Serum amyloid P component	protein	204	7% helix, 47% strand	P02743

Ligands and binding sites

DA · 2'-deoxyadenosine-5'-monophosphate · ligand · 5 copies · chains A, B, C, D, E
CA · Calcium ion · metal · 10 copies · chains A, B, C, D, E

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

Pockets

8 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	70	0.55	0.87	25	empty
2	59	0.53	0.87	25	empty
3	50	0.51	0.88	23	empty
4	78	0.30	0.73	16	empty
5	74	0.30	0.73	14	empty

Interfaces

5 interfaces between chains.

A–E · 762 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 755 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 755 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 753 Å² buried · 10 hydrogen bonds · protein-protein
D–E · 751 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

1LGN · Decameric damp complex of 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 1LGN · PDBe 1LGN · UniProt P02743

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