scPDB - 4qnv entry

Protein Data Bank Entry:

PDB ID : 4qnv

Resolution :2.640 Å

Experimental Method : X-ray

Deposition Date : 2014-06-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	tRNA U34 carboxymethyltransferase
ID:	CMOB_ECOK1
AC:	A1AC32
Organism:	Escherichia coli O1:K1 / APEC
Reign:	Bacteria
TaxID:	405955
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	46.313
Number of residues:	33
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.501	820.125

% Hydrophobic	% Polar
41.98	58.02
According to VolSite

Ligand :

HET Code:	GEK
Formula:	C16H22N6O7S
Molecular weight:	442.447 g/mol
DrugBank ID:	-
Buried Surface Area:	61.32 %
Polar Surface area:	229.9 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
74.1125	-21.162	-14.2218

Binding mode :

What is Poseview ?

2D View
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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
O	NZ	LYS- 91	3.9	0	Ionic (Protein Cationic)	false
OZ1	NZ	LYS- 91	3.13	0	Ionic (Protein Cationic)	false
OZ1	NZ	LYS- 91	3.13	162.55	H-Bond (Protein Donor)	false
O	NZ	LYS- 110	3.37	0	Ionic (Protein Cationic)	false
OXT	NZ	LYS- 110	2.86	0	Ionic (Protein Cationic)	false
OXT	NZ	LYS- 110	2.86	147.22	H-Bond (Protein Donor)	false
N	O	GLY- 130	2.89	158.45	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 152	2.52	145.91	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 152	3.27	136.11	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 152	2.52	148.89	H-Bond (Ligand Donor)	false
C3'	CE1	PHE- 157	4.24	0	Hydrophobic	false
N1	N	ILE- 181	2.92	170.44	H-Bond (Protein Donor)	false
N6	OE2	GLU- 182	2.82	176.67	H-Bond (Ligand Donor)	false
N	O	MET- 196	2.61	171.15	H-Bond (Ligand Donor)	false
C5'	CG2	VAL- 198	4.32	0	Hydrophobic	false
OZ2	OH	TYR- 200	2.74	153.98	H-Bond (Protein Donor)	false
OZ2	NH1	ARG- 315	2.94	162.05	H-Bond (Protein Donor)	false
OZ2	CZ	ARG- 315	3.71	0	Ionic (Protein Cationic)	false