scPDB - 3gc5 entry

Protein Data Bank Entry:

PDB ID : 3gc5

Resolution :1.400 Å

Experimental Method : X-ray

Deposition Date : 2009-02-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Queuine tRNA-ribosyltransferase
ID:	TGT_ZYMMO
AC:	P28720
Organism:	Zymomonas mobilis subsp. mobilis
Reign:	Bacteria
TaxID:	264203
EC Number:	2.4.2.29

Chains:

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

Ligand binding site composition:

B-Factor:	16.127
Number of residues:	34
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.388	320.625

% Hydrophobic	% Polar
47.37	52.63
According to VolSite

Ligand :

HET Code:	2MQ
Formula:	C12H16N7O
Molecular weight:	274.302 g/mol
DrugBank ID:	-
Buried Surface Area:	71.96 %
Polar Surface area:	135.83 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
16.913	16.6648	20.1417

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
N20	OD1	ASP- 102	3.46	136.68	H-Bond (Ligand Donor)	false
N20	OD2	ASP- 102	2.75	147.22	H-Bond (Ligand Donor)	false
N5	OD1	ASP- 102	2.96	171.83	H-Bond (Ligand Donor)	false
C16	CD2	TYR- 106	3.58	0	Hydrophobic	false
C6	CB	TYR- 106	3.52	0	Hydrophobic	false
DuAr	DuAr	TYR- 106	3.9	0	Aromatic Face/Face	false
N20	OD1	ASP- 156	2.9	158.86	H-Bond (Ligand Donor)	false
C7	SG	CYS- 158	3.71	0	Hydrophobic	false
O19	NE2	GLN- 203	2.96	158.1	H-Bond (Protein Donor)	false
O19	N	GLY- 230	2.83	140.92	H-Bond (Protein Donor)	false
N13	O	LEU- 231	2.79	157.48	H-Bond (Ligand Donor)	false
N14	O	ALA- 232	2.9	151	H-Bond (Ligand Donor)	false
C15	CB	ALA- 232	4.24	0	Hydrophobic	false
C7	CB	MET- 260	4.11	0	Hydrophobic	false
C6	CB	MET- 260	3.82	0	Hydrophobic	false
N18	OD2	ASP- 280	2.75	156.93	H-Bond (Ligand Donor)	false
N18	OD2	ASP- 280	2.75	0	Ionic (Ligand Cationic)	false
N18	OD1	ASP- 280	3.77	0	Ionic (Ligand Cationic)	false
N18	O	HOH- 1063	2.88	162.03	H-Bond (Ligand Donor)	false