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Non-native fold of the putative VPS39 zinc finger domain

Analyse Non-native fold of the putative VPS39 zinc finger domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ZE9
Type: protein
Length: 116 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VAM6/VPS39-like protein
UniProt: Q96JC1
Ligands: ZN

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	VAM6/VPS39-like protein	protein	41	7% helix, 49% strand	Q96JC1
C	VAM6/VPS39-like protein	protein	34	0% helix, 53% strand	Q96JC1

Ligands and binding sites

ZN · Zinc ion · metal · 3 copies · chains A, B, C

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

Interfaces

3 interfaces between chains.

A–C · 682 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 196 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 74 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

6ZE9 · Non-native fold of the putative VPS39 zinc finger domain · the same entry in another collection · chain A against A, TM-score 1.00
Q96JC1 · AlphaFold monomer V2.0 prediction for VAM6/VPS39-like protein (Q96JC1) · a predicted model of the same protein · chain A against A, TM-score 0.40

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 Q96JC1
Elsewhere: RCSB PDB 6ZE9 · PDBe 6ZE9 · UniProt Q96JC1

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