scPDB - 3w0s entry

Protein Data Bank Entry:

PDB ID : 3w0s

Resolution :1.770 Å

Experimental Method : X-ray

Deposition Date : 2012-11-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Hygromycin-B 4-O-kinase
ID:	KHYB_ECOLX
AC:	P00557
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	562
EC Number:	2.7.1.163

Chains:

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

Ligand binding site composition:

B-Factor:	24.505
Number of residues:	35
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	3
Water Molecules:	3
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.730	796.500

% Hydrophobic	% Polar
41.95	58.05
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	40.41 %
Polar Surface area:	322.68 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
22.0893	-11.1652	-5.21932

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'	CD1	LEU- 28	4.45	0	Hydrophobic	false
C1'	CD1	LEU- 28	4.38	0	Hydrophobic	false
O2A	OG	SER- 29	3.43	139.89	H-Bond (Protein Donor)	false
O5'	OG	SER- 29	3.06	136.89	H-Bond (Protein Donor)	false
C5'	CB	ALA- 36	3.5	0	Hydrophobic	false
C5'	CD	ARG- 49	4.46	0	Hydrophobic	false
N6	O	ARG- 93	2.87	134.04	H-Bond (Ligand Donor)	false
N1	N	ALA- 95	2.81	164.71	H-Bond (Protein Donor)	false
O2B	ND2	ASN- 202	3	170.68	H-Bond (Protein Donor)	false
C2'	CD1	ILE- 215	4.08	0	Hydrophobic	false
O1G	MG	MG- 403	2.16	0	Metal Acceptor	false
O1B	MG	MG- 403	2.19	0	Metal Acceptor	false
O2A	MG	MG- 403	2.13	0	Metal Acceptor	false