MolNFT v1 · #163172 · protein

Structure of a functional properdin monomer

6RUS: “Structure of a functional properdin monomer”. X-ray diffraction, 5 ligands (MAN, FUC, BGC), 3 pockets (best druggability 0.44). MolNFT v1 #163172 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6RUS
Type: protein
Length: 454 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Properdin
UniProt: P27918
Ligands: MAN, FUC, BGC, NAG, SO4
Pockets: 3 · best druggability 0.44

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Properdin	protein	234	3% helix, 29% strand	P27918
B	Properdin	protein	220	4% helix, 33% strand	P27918

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 15 copies · chains A, B
FUC · alpha-L-fucopyranose · sugar · 5 copies · chains A, B
BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B
SO4 · Sulfate ion · ion · 2 copies · chains A

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

Pockets

3 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	123	0.44	0.77	21	empty
2	153	0.44	0.75	25	empty
3	104	0.34	0.73	21	empty

Interfaces

1 interface between chains.

A–B · 1140 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 22 disulfide, 20 glycan (disulfide, C-mannosylation, O-glycosylation, N-glycosylation).

Compared structures

6RUS · Structure of a functional properdin monomer · the same entry in another collection · chain B against B, TM-score 1.00
P27918 · AlphaFold monomer V2.0 prediction for properdin (P27918) · a predicted model of the same protein · chain B against A, TM-score 0.85

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 P27918
Elsewhere: RCSB PDB 6RUS · PDBe 6RUS · UniProt P27918

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