MolNFT v1 · #129545 · protein

Yndl in complex with 5 amino acid (pga) complex

5ONJ: “Yndl in complex with 5 amino acid (pga) complex”. X-ray diffraction, 2 ligands (GGL, ZN), 1 pocket (best druggability 0.30). MolNFT v1 #129545 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ONJ
Type: protein
Length: 203 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yndl; (2R,3S,4R,5R,6R)-6-((1R,2R,3S,4R,6S)-4,6-diamino-2,3…
UniProt: A0A164XNU3
Ligands: GGL, ZN
Pockets: 1 · best druggability 0.30

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Yndl	protein	202	37% helix, 23% strand	A0A164XNU3
D	(2R,3S,4R,5R,6R)-6-((1R,2R,3S,4R,6S)-4,6-diamino-2,3- dihydroxycyclohexyloxy)-5-amino-2-(aminomethyl)-tetrahydro-2H-pyran- 3,4-diol	protein	1	0% helix, 0% strand	—

Ligands and binding sites

GGL · Gamma-L-glutamic acid · ligand · 5 copies · chains A, D
ZN · Zinc ion · metal · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	62	0.30	0.75	17	GGL

Interfaces

1 interface between chains.

A–D · 149 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

5ONJ · YnDL in Complex with 5 amino acid (PGA) complex · the same entry in another collection · chain D against D, TM-score 1.00

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 A0A164XNU3
Elsewhere: RCSB PDB 5ONJ · PDBe 5ONJ · UniProt A0A164XNU3

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