scPDB - 1nzd entry

Protein Data Bank Entry:

PDB ID : 1nzd

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2003-02-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	DNA beta-glucosyltransferase
ID:	GSTB_BPT4
AC:	P04547
Organism:	Enterobacteria phage T4
Reign:	Viruses
TaxID:	10665
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	23.058
Number of residues:	51
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	1
Water Molecules:	6
Cofactors:
Metals:	CL

Cavity properties

Ligandability	Volume (Å3)
0.896	661.500

% Hydrophobic	% Polar
44.39	55.61
According to VolSite

Ligand :

HET Code:	UPG
Formula:	C15H22N2O17P2
Molecular weight:	564.286 g/mol
DrugBank ID:	DB01861
Buried Surface Area:	74.03 %
Polar Surface area:	316.82 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	7
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
4.79736	1.28928	26.0979

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
C1C	CG2	VAL- 18	3.87	0	Hydrophobic	false
C4C	CG2	VAL- 18	4.22	0	Hydrophobic	false
C6'	CG1	VAL- 18	4.28	0	Hydrophobic	false
O6'	OE1	GLU- 22	2.76	150.85	H-Bond (Ligand Donor)	false
O3'	O	THR- 99	2.64	171.51	H-Bond (Ligand Donor)	false
O4'	NE2	GLN- 137	3.12	176.15	H-Bond (Protein Donor)	false
O1A	N	SER- 189	3.01	159.6	H-Bond (Protein Donor)	false
O2A	OG	SER- 189	2.63	155.96	H-Bond (Protein Donor)	false
O1B	NH2	ARG- 191	2.85	127.76	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 191	3.56	0	Ionic (Protein Cationic)	false
O1B	CZ	ARG- 195	3.78	0	Ionic (Protein Cationic)	false
O1B	NH1	ARG- 195	2.94	179.35	H-Bond (Protein Donor)	false
N3	O	ILE- 238	2.96	168.1	H-Bond (Ligand Donor)	false
O4	N	ILE- 238	3	148.79	H-Bond (Protein Donor)	false
C1C	CE	MET- 240	4.4	0	Hydrophobic	false
C2C	CG2	VAL- 243	3.74	0	Hydrophobic	false
O2'	OH	TYR- 261	2.87	148.71	H-Bond (Ligand Donor)	false
C2'	CE2	TYR- 261	4.13	0	Hydrophobic	false
C3'	CG2	THR- 267	3.71	0	Hydrophobic	false
O4'	N	LEU- 268	3.05	161.13	H-Bond (Protein Donor)	false
C6'	CB	LEU- 268	3.87	0	Hydrophobic	false
O2B	NE	ARG- 269	3.11	133.02	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 269	2.84	142.62	H-Bond (Protein Donor)	false
O2B	CZ	ARG- 269	3.38	0	Ionic (Protein Cationic)	false
O2C	OE1	GLU- 272	3.27	123.66	H-Bond (Ligand Donor)	false
O2C	OE2	GLU- 272	2.52	157.61	H-Bond (Ligand Donor)	false
O3C	OE1	GLU- 272	2.52	158.49	H-Bond (Ligand Donor)	false
O2B	O	HOH- 363	2.87	179.99	H-Bond (Protein Donor)	false
O4'	O	HOH- 375	2.72	163.72	H-Bond (Ligand Donor)	false
O1A	O	HOH- 401	2.62	179.96	H-Bond (Protein Donor)	false
O1B	O	HOH- 545	2.7	162.24	H-Bond (Protein Donor)	false