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YnDL in Complex with 5 amino acid (PGA) complex

Analyse YnDL in Complex with 5 amino acid (PGA) complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ONJ
Type: protein
Length: 208 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.7
Source: Bacillus subtilis; SYNTHETIC CONSTRUCT
Molecule: YndL; (2R,3S,4R,5R,6R)-6-((1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyloxy)-5-amino…
UniProt: A0A164XNU3
Ligands: ZN

Structure

x-ray diffraction · resolution 1.7 · 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	6	0% helix, 0% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · chains A, D

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

Interfaces

1 interface between chains.

A–D · 655 Å² buried · 32 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 modified (nonstandard).

Compared structures

5ONJ · Yndl in complex with 5 amino acid (pga) complex · the same entry in another collection · chain A against A, 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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