MolNFT v1 · #114470 · protein

Crystal structure of norrin in complex with the cysteine-rich domain of frizzled 4 -methylated form

5BQE: “Crystal structure of norrin in complex with the cysteine-rich domain of frizzled 4 -methylated form”. X-ray diffraction, 2 ligands (NAG, CL), 3 pockets (best druggability 0.55). MolNFT v1 #114470 on GenesisL1: 3D structure, binding…

PDB: 5BQE
Type: protein
Length: 324 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Norrin; Frizzled-4
UniProt: Q00604, Q9ULV1
Ligands: NAG, CL
Pockets: 3 · best druggability 0.55

Structure

x-ray diffraction · 2 distinct chains · 23% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Norrin	protein	101	0% helix, 62% strand	Q00604
C	Frizzled-4	protein	122	42% helix, 10% strand	Q9ULV1

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C
CL · Chloride ion · ion · chains C
PG0 · 2-(2-methoxyethoxy)ethanol · additive · 3 copies · chains A, B, C

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

Pockets

3 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	74	0.55	0.87	24	empty
2	156	0.48	0.77	15	empty
3	93	0.38	0.76	17	empty

Interfaces

2 interfaces between chains.

A–B · 1781 Å² buried · 25 hydrogen bonds · protein-protein
A–C · 941 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 6 modified, 1 glycan (disulfide, methylation, N-glycosylation).

Compared structures

Q9ULV1 · AlphaFold monomer V2.0 prediction for frizzled-4 (Q9ULV1) · a predicted model of the same protein · chain C against A, TM-score 0.97
Q00604 · AlphaFold monomer V2.0 prediction for norrin (Q00604) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 Q00604
Every structure of UniProt Q9ULV1
Elsewhere: RCSB PDB 5BQE · PDBe 5BQE · UniProt Q00604 · UniProt Q9ULV1

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