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Crystal structure of native octameric sap-like pentraxin from limulus polyphemus

Analyse Crystal structure of native octameric sap-like pentraxin from limulus polyphemus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3FLR
Type: protein
Length: 434 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sap-like pentraxin
UniProt: Q8WQK3
Ligands: CA
Pockets: 2 · best druggability 0.48

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Sap-like pentraxin	protein	217	5% helix, 48% strand	Q8WQK3

Ligands and binding sites

CA · Calcium ion · metal · 4 copies · chains A, B

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

Pockets

2 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	113	0.48	0.80	21	empty
2	146	0.48	0.78	31	empty

Interfaces

1 interface between chains.

A–B · 604 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

3FLR · Crystal structure of native octameric SAP-like pentraxin from Limulus polyphemus · the same entry in another collection · 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 Q8WQK3
Elsewhere: RCSB PDB 3FLR · PDBe 3FLR · UniProt Q8WQK3

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