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PylC in complex with L-lysine-Ne-D-ornithine (cocrystallized with L-lysine-Ne-D-ornithine)

Analyse PylC in complex with L-lysine-Ne-D-ornithine (cocrystallized with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4FFM
Type: protein
Length: 344 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.91
Source: Methanosarcina barkeri
Molecule: PylC
UniProt: Q46E79
Ligands: 0TF, ADP, ATP, MG
Pockets: 1 · best druggability 0.72

Structure

x-ray diffraction · resolution 1.91 · 1 distinct chain · 31% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	PylC	protein	344	31% helix, 32% strand	Q46E79

Ligands and binding sites

0TF · N~6~-D-ornithyl-L-lysine · ligand · chains A
ADP · Adenosine-5'-diphosphate · ligand · chains A
ATP · Adenosine-5'-triphosphate · ligand · chains A
MG · Magnesium ion · metal · 2 copies · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	599	0.72	0.80	61	0TF, ADP, MG, ATP

Compared structures

4FFM · Pylc in complex with L-lysine-ne-D-ornithine (cocrystallized with L… · 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 Q46E79
Elsewhere: RCSB PDB 4FFM · PDBe 4FFM · UniProt Q46E79

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