scPDB - 2zxu entry

Protein Data Bank Entry:

PDB ID : 2zxu

Resolution :2.750 Å

Experimental Method : X-ray

Deposition Date : 2009-01-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	tRNA dimethylallyltransferase
ID:	MIAA_ECOLI
AC:	P16384
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	2.5.1.75

Chains:

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

Ligand binding site composition:

B-Factor:	27.867
Number of residues:	31
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.738	901.125

% Hydrophobic	% Polar
38.20	61.80
According to VolSite

Ligand :

HET Code:	DST
Formula:	C5H11O6P2S
Molecular weight:	261.150 g/mol
DrugBank ID:	DB02270
Buried Surface Area:	64.42 %
Polar Surface area:	157.47 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	0
Rings:	0
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
13.1816	58.1543	43.1099

Binding mode :

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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
S9	OG1	THR- 19	2.67	154.76	Weak HBond PROT	false
C14	CB	THR- 19	3.5	0	Hydrophobic	false
S9	CB	THR- 19	3.68	0	Hydrophobic	false
O2	N	ALA- 20	2.99	163.32	H-Bond (Protein Donor)	false
O4	N	GLY- 22	3.12	145.62	H-Bond (Protein Donor)	false
O6	NZ	LYS- 23	3.3	146.06	H-Bond (Protein Donor)	false
O6	N	LYS- 23	2.62	141.23	H-Bond (Protein Donor)	false
O8	NZ	LYS- 23	2.83	150.32	H-Bond (Protein Donor)	false
O6	NZ	LYS- 23	3.3	0	Ionic (Protein Cationic)	false
O8	NZ	LYS- 23	2.83	0	Ionic (Protein Cationic)	false
C10	CB	ALA- 55	3.51	0	Hydrophobic	false
O4	NH1	ARG- 217	3.33	122.68	H-Bond (Protein Donor)	false
O4	NH2	ARG- 217	2.65	152.72	H-Bond (Protein Donor)	false
O2	NH1	ARG- 217	3.2	166.29	H-Bond (Protein Donor)	false
O4	CZ	ARG- 217	3.34	0	Ionic (Protein Cationic)	false
C13	CE	MET- 221	4.21	0	Hydrophobic	false
C13	CG2	VAL- 249	3.99	0	Hydrophobic	false
C14	CG2	VAL- 249	3.84	0	Hydrophobic	false
C13	CG2	THR- 275	3.83	0	Hydrophobic	false
C14	CG2	THR- 275	3.77	0	Hydrophobic	false
C14	CD1	LEU- 278	3.72	0	Hydrophobic	false
O5	MG	MG- 318	2.03	0	Metal Acceptor	false
O7	MG	MG- 318	2.01	0	Metal Acceptor	false