Research workbench

Xenopus ZNRF3 ectodomain crystal form I

Analyse Xenopus ZNRF3 ectodomain crystal form I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4C8T
Type: protein
Length: 291 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.4
Source: XENOPUS (SILURANA) TROPICALIS
Molecule: E3 ubiquitin-protein ligase ZNRF3
EC: 6.3.2.-
UniProt: Q08D68
Pockets: 5 · best druggability 0.49

Structure

x-ray diffraction · resolution 2.4 · 2 distinct chains · 23% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	E3 ubiquitin-protein ligase ZNRF3 (EC 6.3.2.-)	protein	146	25% helix, 38% strand	Q08D68
B	E3 ubiquitin-protein ligase ZNRF3 (EC 6.3.2.-)	protein	145	21% helix, 41% strand	Q08D68

Pockets

5 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	93	0.49	0.82	23	empty
2	84	0.49	0.83	15	empty
3	86	0.47	0.81	15	empty
4	120	0.39	0.75	23	empty
5	95	0.35	0.74	16	empty

Interfaces

1 interface between chains.

A–B · 1175 Å² buried · 32 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

4C8T · Xenopus ZNRF3 ectodomain crystal form I · the same entry in another collection · chain A against A, TM-score 1.00
Q08D68 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase ZNRF3 (Q08D68) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 Q08D68
Elsewhere: RCSB PDB 4C8T · PDBe 4C8T · UniProt Q08D68

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