Research workbench

C1R homodimer CUB1-EGF-CUB2

Analyse C1R homodimer CUB1-EGF-CUB2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6F39
Type: protein
Length: 555 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Complement C1R subcomponent
EC: 3.4.21.41
UniProt: P00736
Ligands: NAG, MAN, BMA, GAL, CA, NA
Pockets: 10 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 1% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Complement C1R subcomponent (EC 3.4.21.41)	protein	275	0% helix, 34% strand	P00736
B	Complement C1R subcomponent (EC 3.4.21.41)	protein	280	1% helix, 30% strand	P00736

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
MAN · alpha-D-mannopyranose · sugar · 4 copies
BMA · beta-D-mannopyranose · sugar · 2 copies
GAL · beta-D-galactopyranose · sugar · 2 copies
CA · Calcium ion · metal · 6 copies · chains A, B
NA · Sodium ion · metal · 2 copies · chains A, B

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

Pockets

10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	285	0.81	0.91	40	empty
2	234	0.79	0.92	31	empty
3	1039	0.73	0.76	76	empty
4	997	0.73	0.76	68	empty
5	196	0.72	0.88	27	empty

Interfaces

1 interface between chains.

A–B · 1019 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

6F39 · C1r homodimer CUB1-EGF-CUB2 · the same entry in another collection · chain A against A, TM-score 1.00
P00736 · AlphaFold monomer V2.0 prediction for complement C1R subcomponent (P00736) · a predicted model of the same protein · chain B against A, TM-score 0.76

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 P00736
Elsewhere: RCSB PDB 6F39 · PDBe 6F39 · UniProt P00736

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