scPDB - 2okc entry

Protein Data Bank Entry:

PDB ID : 2okc

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2007-01-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Probable type I restriction enzyme BthVORF4518P M protein
ID:	T1M_BACTN
AC:	Q89Z59
Organism:	Bacteroides thetaiotaomicron
Reign:	Bacteria
TaxID:	226186
EC Number:	2.1.1.72

Chains:

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

Ligand binding site composition:

B-Factor:	44.783
Number of residues:	39
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.544	425.250

% Hydrophobic	% Polar
38.10	61.90
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	81.26 %
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
85.8823	53.4058	115.5

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
C3'	CD1	TYR- 152	3.77	0	Hydrophobic	false
N	OG1	THR- 154	2.84	166.12	H-Bond (Ligand Donor)	false
CB	CB	THR- 154	4.31	0	Hydrophobic	false
O	CZ	ARG- 156	3.7	0	Ionic (Protein Cationic)	false
O	NH1	ARG- 156	2.97	133.52	H-Bond (Protein Donor)	false
C4'	CB	ALA- 178	4.26	0	Hydrophobic	false
C1'	CB	ALA- 178	4.47	0	Hydrophobic	false
O	OG1	THR- 181	3.32	127.74	H-Bond (Protein Donor)	false
OXT	OG1	THR- 181	2.64	140.13	H-Bond (Protein Donor)	false
OXT	N	THR- 181	3.2	130.04	H-Bond (Protein Donor)	false
O	N	GLY- 183	2.97	131.55	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 214	2.75	170.42	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 214	2.87	158.12	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 214	3.4	126.55	H-Bond (Ligand Donor)	false
N3	N	ASN- 215	3.39	141.28	H-Bond (Protein Donor)	false
O2'	OG1	THR- 216	3.35	172.58	H-Bond (Protein Donor)	false
N6	OD1	ASP- 243	2.78	156.18	H-Bond (Ligand Donor)	false
N1	N	SER- 244	3.14	142.26	H-Bond (Protein Donor)	false
CE	CB	ASN- 259	4.33	0	Hydrophobic	false
N6	O	HOH- 558	3.37	139.26	H-Bond (Ligand Donor)	false
N	O	HOH- 576	2.98	174.5	H-Bond (Ligand Donor)	false