scPDB - 1kws entry

Protein Data Bank Entry:

PDB ID : 1kws

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2002-01-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 3
ID:	B3GA3_HUMAN
AC:	O94766
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	17.940
Number of residues:	39
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
0.465	867.375

% Hydrophobic	% Polar
41.25	58.75
According to VolSite

Ligand :

HET Code:	UGA
Formula:	C15H19N2O18P2
Molecular weight:	577.261 g/mol
DrugBank ID:	DB03041
Buried Surface Area:	67.5 %
Polar Surface area:	336.72 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	3
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
23.2899	-0.855027	14.3216

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
O3D	O	PRO- 82	2.64	151.6	H-Bond (Ligand Donor)	false
C1D	CG	PRO- 82	3.86	0	Hydrophobic	false
C4D	CG	PRO- 82	3.7	0	Hydrophobic	false
C2D	CE2	TYR- 84	3.77	0	Hydrophobic	false
C1D	CD2	TYR- 84	4.15	0	Hydrophobic	false
N3	OD2	ASP- 113	3.09	158.22	H-Bond (Ligand Donor)	false
O'P	N	ARG- 156	2.78	159	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 156	3.1	0	Ionic (Protein Cationic)	false
C5D	CB	ARG- 156	4.47	0	Hydrophobic	false
O4'	NH2	ARG- 161	2.98	135.77	H-Bond (Protein Donor)	false
O3'	OD1	ASP- 194	2.89	136.05	H-Bond (Ligand Donor)	false
C3D	CB	ASP- 194	3.77	0	Hydrophobic	false
O3D	N	ASP- 195	2.82	163.9	H-Bond (Protein Donor)	false
O2D	OD1	ASP- 195	2.79	172.27	H-Bond (Ligand Donor)	false
O2D	OD2	ASP- 195	3.31	128.25	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 252	3.5	129.96	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 252	2.5	171.67	H-Bond (Ligand Donor)	false
C3'	CB	MET- 253	4.35	0	Hydrophobic	false
C4'	CD2	LEU- 280	4.34	0	Hydrophobic	false
O2'	NE2	HIS- 308	2.67	138.14	H-Bond (Protein Donor)	false
O3B	NE2	HIS- 308	3.23	138.31	H-Bond (Protein Donor)	false
O1B	NH1	ARG- 310	2.95	134.39	H-Bond (Protein Donor)	false
O1B	MN	MN- 500	2.11	0	Metal Acceptor	false
O1A	MN	MN- 500	2.13	0	Metal Acceptor	false
O2'	O	HOH- 503	2.91	138.75	H-Bond (Protein Donor)	false