MolNFT v1 · #173507 · protein

CIRPA1 in complex with pseudo-monomeric properdin lacking TSR2-3

7B26: “CIRPA1 in complex with pseudo-monomeric properdin lacking TSR2-3”. X-ray diffraction, 4 ligands (MAN, FUC, BGC), 4 pockets (best druggability 0.62). MolNFT v1 #173507 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7B26
Type: protein
Length: 453 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Properdin; CIRPA1
UniProt: P27918
Ligands: MAN, FUC, BGC, BMA
Pockets: 4 · best druggability 0.62

Structure

x-ray diffraction · 3 distinct chains · 5% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Properdin	protein	191	0% helix, 37% strand	P27918
A	Properdin	protein	106	4% helix, 45% strand	P27918
C	CIRPA1	protein	156	12% helix, 46% strand	—

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 8 copies · chains B, A
FUC · alpha-L-fucopyranose · sugar · chains B
BGC · beta-D-glucopyranose · sugar · chains B, A
BMA · beta-D-mannopyranose · sugar · chains B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	221	0.62	0.82	28	empty
2	145	0.46	0.77	26	empty
3	153	0.43	0.75	24	empty
4	106	0.41	0.76	20	empty

Interfaces

2 interfaces between chains.

B–A · 1186 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 910 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 17 disulfide, 10 glycan (disulfide, C-mannosylation, O-glycosylation).

Compared structures

7B26 · CirpA1 in complex with pseudo-monomeric Properdin lacking TSR2-3 · 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 A against A, TM-score 0.94

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 7B26 · PDBe 7B26 · UniProt P27918

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