MolNFT v1 · #87856 · protein

Structure of ZNRF3-RSPO1

4CDK · E3 ubiquitin-protein ligase ZNRF3: “Structure of ZNRF3-RSPO1”. X-ray diffraction, 17 pockets (best druggability 0.76). MolNFT v1 #87856 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4CDK
Type: protein
Length: 1,040 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase ZNRF3; R-spondin-1
UniProt: Q5SSZ7, Q2MKA7
Pockets: 17 · best druggability 0.76

Structure

x-ray diffraction · 8 distinct chains · 14% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	E3 ubiquitin-protein ligase ZNRF3	protein	152	24% helix, 36% strand	Q5SSZ7
B	E3 ubiquitin-protein ligase ZNRF3	protein	156	22% helix, 35% strand	Q5SSZ7
C	E3 ubiquitin-protein ligase ZNRF3	protein	155	22% helix, 35% strand	Q5SSZ7
D	E3 ubiquitin-protein ligase ZNRF3	protein	152	24% helix, 36% strand	Q5SSZ7
E	R-spondin-1	protein	110	0% helix, 42% strand	Q2MKA7
F	R-spondin-1	protein	103	0% helix, 41% strand	Q2MKA7
G	R-spondin-1	protein	107	0% helix, 40% strand	Q2MKA7
H	R-spondin-1	protein	105	0% helix, 36% strand	Q2MKA7

Pockets

17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1165	0.76	0.78	97	empty
2	74	0.68	0.94	16	empty
3	362	0.62	0.78	45	empty
4	262	0.62	0.80	38	empty
5	172	0.60	0.82	35	empty

Interfaces

12 interfaces between chains.

A–B · 1268 Å² buried · 29 hydrogen bonds · protein-protein
C–D · 1258 Å² buried · 31 hydrogen bonds · protein-protein
C–G · 1248 Å² buried · 17 hydrogen bonds · protein-protein
A–E · 1186 Å² buried · 17 hydrogen bonds · protein-protein
B–F · 1008 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 34 disulfide (disulfide).

Compared structures

4CDK · Structure of ZNRF3-RSPO1 · the same entry in another collection · chain H against H, TM-score 1.00
Q5SSZ7 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase ZNRF3 (Q5SSZ7) · a predicted model of the same protein · chain D 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 Q5SSZ7
Every structure of UniProt Q2MKA7
Elsewhere: RCSB PDB 4CDK · PDBe 4CDK · UniProt Q5SSZ7 · UniProt Q2MKA7

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