scPDB - 3vd7 entry

Protein Data Bank Entry:

PDB ID : 3vd7

Resolution :2.870 Å

Experimental Method : X-ray

Deposition Date : 2012-01-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Beta-galactosidase
ID:	BGAL_ECOLI
AC:	P00722
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	3.2.1.23

Chains:

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

Ligand binding site composition:

B-Factor:	32.118
Number of residues:	24
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	MG NA

Cavity properties

Ligandability	Volume (Å3)
0.130	823.500

% Hydrophobic	% Polar
40.16	59.84
According to VolSite

Ligand :

HET Code:	GTZ
Formula:	C6H10N4O4
Molecular weight:	202.168 g/mol
DrugBank ID:	DB02294
Buried Surface Area:	72.56 %
Polar Surface area:	124.52 Å2

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

Mass center Coordinates

X	Y	Z
124.408	10.5327	33.553

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
C4	CB	ASP- 201	4.47	0	Hydrophobic	false
O4	OD2	ASP- 201	2.67	154.29	H-Bond (Ligand Donor)	false
C2	SD	MET- 502	4.07	0	Hydrophobic	false
C2	CE1	TYR- 503	4.21	0	Hydrophobic	false
O2	OE2	GLU- 537	2.75	157.88	H-Bond (Ligand Donor)	false
O3	OE2	GLU- 537	3.1	126.47	H-Bond (Ligand Donor)	false
O6	NE2	HIS- 540	2.57	149.49	H-Bond (Ligand Donor)	false
C3	CZ2	TRP- 568	4.13	0	Hydrophobic	false
C4	CE2	TRP- 568	3.86	0	Hydrophobic	false
C6	CD2	PHE- 601	4.48	0	Hydrophobic	false
C5	CH2	TRP- 999	4.03	0	Hydrophobic	false
C6	CZ3	TRP- 999	4.13	0	Hydrophobic	false