scPDB - 4r29 entry

Protein Data Bank Entry:

PDB ID : 4r29

Resolution :2.310 Å

Experimental Method : X-ray

Deposition Date : 2014-08-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uncharacterized protein
ID:	Q7DBA6_ECO57
AC:	Q7DBA6
Organism:	Escherichia coli O157:H7
Reign:	Bacteria
TaxID:	83334
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	23.005
Number of residues:	37
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.529	722.250

% Hydrophobic	% Polar
46.73	53.27
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	67.44 %
Polar Surface area:	189.77 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
30.4965	-0.566111	42.569

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
N	OG	SER- 98	2.81	145.37	H-Bond (Ligand Donor)	false
O	CZ	ARG- 107	3.61	0	Ionic (Protein Cationic)	false
OXT	CZ	ARG- 107	3.38	0	Ionic (Protein Cationic)	false
O	NH2	ARG- 107	2.71	159.11	H-Bond (Protein Donor)	false
OXT	NH2	ARG- 107	3.19	133.3	H-Bond (Protein Donor)	false
OXT	NH1	ARG- 107	2.71	160.48	H-Bond (Protein Donor)	false
N	O	GLN- 111	2.77	165.81	H-Bond (Ligand Donor)	false
O	N	GLN- 111	2.93	173.38	H-Bond (Protein Donor)	false
O3'	OE2	GLU- 191	3.01	154.73	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 191	3.06	134.31	H-Bond (Ligand Donor)	false
C2'	CB	ALA- 195	4.19	0	Hydrophobic	false
C4'	CB	MET- 198	4.02	0	Hydrophobic	false
C1'	CB	MET- 198	3.55	0	Hydrophobic	false
CB	CZ	PHE- 202	3.82	0	Hydrophobic	false
C4'	CE2	PHE- 202	3.77	0	Hydrophobic	false
C5'	CE2	PHE- 202	3.78	0	Hydrophobic	false
OXT	OH	TYR- 204	2.75	126.55	H-Bond (Protein Donor)	false
C5'	CE2	TYR- 204	4.08	0	Hydrophobic	false
N6	O	GLU- 208	2.98	133.55	H-Bond (Ligand Donor)	false
C3'	CZ	TYR- 212	4.29	0	Hydrophobic	false
C2'	CE2	TYR- 212	3.74	0	Hydrophobic	false
DuAr	DuAr	TYR- 212	3.68	0	Aromatic Face/Face	false