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GID4 in complex with iglwks peptide

Analyse GID4 in complex with iglwks peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WZX
Type: protein
Length: 340 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glucose-induced degradation protein 4 homolog; Ile-gly-leu-TRP-lys peptide
UniProt: Q8IVV7
Ligands: UNX
Pockets: 3 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 13% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Glucose-induced degradation protein 4 homolog	protein	165	13% helix, 47% strand	Q8IVV7
C, D	Ile-gly-leu-TRP-lys peptide	protein	5	0% helix, 60% strand	—

Ligands and binding sites

UNX · Unknown atom or ion · ion · 16 copies · chains A, B

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	251	0.63	0.82	35	empty
2	102	0.41	0.76	21	UNX
3	77	0.36	0.76	21	empty

Interfaces

3 interfaces between chains.

A–B · 656 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 512 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 370 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

6WZX · GID4 in complex with IGLWKS peptide · the same entry in another collection · chain A against A, TM-score 1.00
Q8IVV7 · AlphaFold monomer V2.0 prediction for glucose-induced degradation protein 4 homolog… · a predicted model of the same protein · chain B against A, TM-score 0.98

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 Q8IVV7
Elsewhere: RCSB PDB 6WZX · PDBe 6WZX · UniProt Q8IVV7

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