scPDB - 3o3p entry

Protein Data Bank Entry:

PDB ID : 3o3p

Resolution :2.530 Å

Experimental Method : X-ray

Deposition Date : 2010-07-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glycosyl transferase, family 2
ID:	Q1ATN7_RUBXD
AC:	Q1ATN7
Organism:	Rubrobacter xylanophilus
Reign:	Bacteria
TaxID:	266117
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	39.532
Number of residues:	46
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.698	840.375

% Hydrophobic	% Polar
36.95	63.05
According to VolSite

Ligand :

HET Code:	GDD
Formula:	C16H23N5O16P2
Molecular weight:	603.325 g/mol
DrugBank ID:	-
Buried Surface Area:	69.4 %
Polar Surface area:	352.71 Å2

Number of
H-Bond Acceptors:	19
H-Bond Donors:	8
Rings:	4
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
43.8234	-23.5594	-5.58987

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
C1'	CB	PRO- 49	4.36	0	Hydrophobic	false
O3'	O	PRO- 49	3.05	169.38	H-Bond (Ligand Donor)	false
C1'	CB	ARG- 51	4.45	0	Hydrophobic	false
O2'	N	ARG- 51	2.97	140.5	H-Bond (Protein Donor)	false
N2	O	VAL- 80	3.01	138.54	H-Bond (Ligand Donor)	false
N2	OE1	GLU- 102	2.95	134.41	H-Bond (Ligand Donor)	false
N1	OE1	GLU- 102	2.73	150.58	H-Bond (Ligand Donor)	false
C1'	CG	LYS- 115	4.42	0	Hydrophobic	false
C31	CD	LYS- 115	4.4	0	Hydrophobic	false
C5'	CD	LYS- 115	4.19	0	Hydrophobic	false
O31	NZ	LYS- 115	3.13	122.08	H-Bond (Protein Donor)	false
C4'	CB	ASP- 135	4.4	0	Hydrophobic	false
O31	OD2	ASP- 135	3.37	173.3	H-Bond (Ligand Donor)	false
O3'	N	ALA- 136	2.98	145.57	H-Bond (Protein Donor)	false
C3'	CB	ASP- 137	4.23	0	Hydrophobic	false
O21	O	LEU- 207	3.01	154.8	H-Bond (Ligand Donor)	false
C61	CB	LEU- 207	3.74	0	Hydrophobic	false
O1A	OH	TYR- 227	2.67	137.05	H-Bond (Protein Donor)	false
C51	CD1	TYR- 227	4.48	0	Hydrophobic	false
O6A	O	TYR- 227	2.93	171.93	H-Bond (Ligand Donor)	false
O41	OE2	GLU- 230	3.03	143.23	H-Bond (Ligand Donor)	false
C41	CG	GLU- 230	3.59	0	Hydrophobic	false
O2B	ND2	ASN- 256	3.23	137.21	H-Bond (Protein Donor)	false
O3B	NE2	GLN- 259	2.65	153.9	H-Bond (Protein Donor)	false
C51	CE	MET- 267	3.83	0	Hydrophobic	false
O2A	MG	MG- 339	2.69	0	Metal Acceptor	false
O2B	MG	MG- 339	2.33	0	Metal Acceptor	false