scPDB - 3vqx entry

Protein Data Bank Entry:

PDB ID : 3vqx

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2012-04-02

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
D	100 %

Ligand binding site composition:

B-Factor:	42.528
Number of residues:	46
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.402	610.875

% Hydrophobic	% Polar
49.17	50.83
According to VolSite

Ligand :

HET Code:	BLK
Formula:	C21H34N7O10P
Molecular weight:	575.509 g/mol
DrugBank ID:	-
Buried Surface Area:	64.62 %
Polar Surface area:	270.74 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
52.4348	10.7546	27.5116

Binding mode :

What is Poseview ?

2D View
3D View

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
CT2	CB	ALA- 302	4.05	0	Hydrophobic	false
CT2	CB	LEU- 305	3.9	0	Hydrophobic	false
CT1	CZ	TYR- 306	3.5	0	Hydrophobic	false
CT2	CD1	TYR- 306	4.31	0	Hydrophobic	false
CT3	CD1	LEU- 309	4.31	0	Hydrophobic	false
O2P	CZ	ARG- 330	3.39	0	Ionic (Protein Cationic)	false
N1	N	LEU- 339	3.23	169.07	H-Bond (Protein Donor)	false
N6	O	LEU- 339	3.35	143.57	H-Bond (Ligand Donor)	false
DuAr	DuAr	PHE- 342	3.68	0	Aromatic Face/Face	false
C5'	CE	MET- 344	3.97	0	Hydrophobic	false
C4'	SD	MET- 344	3.84	0	Hydrophobic	false
C1'	SD	MET- 344	3.5	0	Hydrophobic	false
NZ	OD1	ASN- 346	2.66	125.55	H-Bond (Ligand Donor)	false
O3'	OE2	GLU- 396	2.69	149.47	H-Bond (Ligand Donor)	false
O2'	O	LEU- 397	3.02	120.23	H-Bond (Ligand Donor)	false
CB	CB	SER- 399	3.71	0	Hydrophobic	false
CG	CG1	VAL- 401	3.84	0	Hydrophobic	false
CT1	CH2	TRP- 417	3.37	0	Hydrophobic	false
CT	CZ3	TRP- 417	3.83	0	Hydrophobic	false
CT3	CE3	TRP- 417	3.82	0	Hydrophobic	false
O2'	N	GLY- 423	3.05	128.31	H-Bond (Protein Donor)	false
C2'	CD	ARG- 426	3.61	0	Hydrophobic	false
O2'	NH1	ARG- 426	3.49	131.96	H-Bond (Protein Donor)	false
N3	O	HOH- 621	3.33	179.96	H-Bond (Protein Donor)	false