MolNFT v1 · #145072 · protein

Complex of GID4 fragment with short peptide

6CD8 · Glucose-induced degradation protein 4 homolog: “Complex of GID4 fragment with short peptide”. X-ray diffraction, 1 ligand (UNX), 5 pockets (best druggability 0.43). MolNFT v1 #145072 on GenesisL1: 3D structure, binding sites and…

PDB: 6CD8
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; Tetrapeptide psrv
UniProt: Q8IVV7
Ligands: UNX
Pockets: 5 · best druggability 0.43

Structure

x-ray diffraction · 3 distinct chains · 12% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glucose-induced degradation protein 4 homolog	protein	167	13% helix, 44% strand	Q8IVV7
B	Glucose-induced degradation protein 4 homolog	protein	165	12% helix, 45% strand	Q8IVV7
C, D	Tetrapeptide psrv	protein	4	0% helix, 50% strand	—

Ligands and binding sites

UNX · Unknown atom or ion · ion · 19 copies · chains A, B

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

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	108	0.43	0.77	27	UNX
2	170	0.42	0.74	31	empty
3	62	0.40	0.78	15	UNX
4	77	0.36	0.77	15	empty
5	87	0.35	0.75	16	empty

Interfaces

5 interfaces between chains.

A–C · 390 Å² buried · 12 hydrogen bonds · protein-protein
B–D · 362 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 202 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 49 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 16 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6CD8 · Complex of GID4 fragment with short 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 0.99

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 6CD8 · PDBe 6CD8 · UniProt Q8IVV7

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