scPDB - 4z0u entry

Protein Data Bank Entry:

PDB ID : 4z0u

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2015-03-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ribonuclease H
ID:	RNH_ECO24
AC:	A7ZHV1
Organism:	Escherichia coli O139:H28
Reign:	Bacteria
TaxID:	331111
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	40.988
Number of residues:	20
Including
Standard Amino Acids:	19
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.212	276.750

% Hydrophobic	% Polar
52.44	47.56
According to VolSite

Ligand :

HET Code:	ASP_ILE_PRO_PHE
Formula:	C24H33N4O7
Molecular weight:	489.541 g/mol
DrugBank ID:	-
Buried Surface Area:	49.06 %
Polar Surface area:	186.4 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	3
Rings:	2
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
86.0081	44.3992	30.2215

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
O	NZ	LYS- 3	2.57	173.85	H-Bond (Protein Donor)	false
OD1	NZ	LYS- 3	3.6	0	Ionic (Protein Cationic)	false
CB	CD	LYS- 3	4.18	0	Hydrophobic	false
CG	CG2	VAL- 5	3.8	0	Hydrophobic	false
CE2	CG1	VAL- 5	4.06	0	Hydrophobic	false
CG	CD2	LEU- 26	3.63	0	Hydrophobic	false
CZ	CB	LEU- 26	3.89	0	Hydrophobic	false
CD1	CB	TYR- 28	4.43	0	Hydrophobic	false
CG	CG	TYR- 28	4.38	0	Hydrophobic	false
CG1	CD2	TYR- 28	4.08	0	Hydrophobic	false
CE2	CB	TYR- 28	3.65	0	Hydrophobic	false
CD1	CB	ARG- 31	3.82	0	Hydrophobic	false
OXT	NZ	LYS- 33	4	0	Ionic (Protein Cationic)	false
CE1	CB	LYS- 33	3.79	0	Hydrophobic	false
CB	CD2	LEU- 59	4.22	0	Hydrophobic	false
CD2	CD2	LEU- 59	3.92	0	Hydrophobic	false
O	N	LYS- 60	2.93	164.77	H-Bond (Protein Donor)	false
OXT	NZ	LYS- 60	3.99	0	Ionic (Protein Cationic)	false
CB	CG	GLU- 61	3.79	0	Hydrophobic	false
CB	SG	CYS- 63	3.85	0	Hydrophobic	false