scPDB - 2zce entry

Protein Data Bank Entry:

PDB ID : 2zce

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2007-11-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pyrrolysine--tRNA ligase
ID:	PYLS_METMA
AC:	Q8PWY1
Organism:	Methanosarcina mazei
Reign:	Archaea
TaxID:	192952
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	35.540
Number of residues:	35
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:	ANP
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
1.017	465.750

% Hydrophobic	% Polar
56.52	43.48
According to VolSite

Ligand :

HET Code:	PYL
Formula:	C12H21N3O3
Molecular weight:	255.313 g/mol
DrugBank ID:	-
Buried Surface Area:	75.7 %
Polar Surface area:	109.22 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	2
Rings:	1
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
7.86172	73.7889	3.22761

Binding mode :

What is Poseview ?

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Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
CB2	CB	ALA- 302	4.48	0	Hydrophobic	false
CB2	CB	LEU- 305	3.67	0	Hydrophobic	false
CB2	CG	TYR- 306	4.38	0	Hydrophobic	false
CD2	CZ	TYR- 306	3.56	0	Hydrophobic	false
CB2	CD1	LEU- 309	4.09	0	Hydrophobic	false
O	NH2	ARG- 330	3.17	130	H-Bond (Protein Donor)	false
O2	ND2	ASN- 346	2.81	176.45	H-Bond (Protein Donor)	false
CB2	SG	CYS- 348	4.1	0	Hydrophobic	false
CD	CG1	VAL- 401	3.66	0	Hydrophobic	false
CG2	CZ3	TRP- 417	3.79	0	Hydrophobic	false
CD2	CH2	TRP- 417	3.38	0	Hydrophobic	false
CB	C5'	ANP- 501	4.19	0	Hydrophobic	false
N	O	HOH- 809	2.69	145.87	H-Bond (Ligand Donor)	false