scPDB - 3okx entry

Protein Data Bank Entry:

PDB ID : 3okx

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2010-08-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	S-adenosyl-L-methionine-binding protein RPA0152
ID:	Y152_RHOPA
AC:	Q6NDF6
Organism:	Rhodopseudomonas palustris
Reign:	Bacteria
TaxID:	258594
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	14 %
B	86 %

Ligand binding site composition:

B-Factor:	17.848
Number of residues:	39
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.886	820.125

% Hydrophobic	% Polar
47.74	52.26
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	77.03 %
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
23.1457	-15.6438	22.8151

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'	CD2	LEU- 37	3.72	0	Hydrophobic	false
C3'	CB	CYS- 40	3.77	0	Hydrophobic	false
O3'	O	PRO- 41	2.67	154.53	H-Bond (Ligand Donor)	false
N	ND1	HIS- 43	3.28	148.92	H-Bond (Ligand Donor)	false
N6	ND1	HIS- 79	2.97	159.3	H-Bond (Ligand Donor)	false
N1	N	ARG- 80	3.07	159.32	H-Bond (Protein Donor)	false
OXT	NH2	ARG- 103	3.3	135.31	H-Bond (Protein Donor)	false
OXT	NE	ARG- 103	2.83	168.28	H-Bond (Protein Donor)	false
OXT	CZ	ARG- 103	3.51	0	Ionic (Protein Cationic)	false
SD	CB	PRO- 105	4.01	0	Hydrophobic	false
C4'	CG	PRO- 105	4.14	0	Hydrophobic	false
C1'	CG	PRO- 105	4.01	0	Hydrophobic	false
N	O	THR- 113	2.9	125.08	H-Bond (Ligand Donor)	false
O	N	THR- 113	3.03	173.26	H-Bond (Protein Donor)	false
N	OD2	ASP- 132	2.63	162.72	H-Bond (Ligand Donor)	false
N	OD2	ASP- 132	2.63	0	Ionic (Ligand Cationic)	false
N	OD1	ASP- 132	3.94	0	Ionic (Ligand Cationic)	false
N7	N	LEU- 134	2.94	163.48	H-Bond (Protein Donor)	false
N6	OG1	THR- 137	2.91	152.63	H-Bond (Ligand Donor)	false
O3'	NZ	LYS- 156	2.91	158.31	H-Bond (Protein Donor)	false
O2'	NZ	LYS- 156	2.89	122.2	H-Bond (Protein Donor)	false
N	O	HOH- 216	3.04	122.67	H-Bond (Ligand Donor)	false