scPDB - 2zif entry

Protein Data Bank Entry:

PDB ID : 2zif

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2008-02-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Methyltransferase
ID:	Q5SL84_THET8
AC:	Q5SL84
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	300852
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	44.224
Number of residues:	31
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.420	526.500

% Hydrophobic	% Polar
51.28	48.72
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	66.83 %
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
46.0736	36.3495	42.8756

Binding mode :

What is Poseview ?

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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
N6	OD1	ASP- 28	2.6	138.83	H-Bond (Ligand Donor)	false
N1	N	ALA- 29	2.57	172.95	H-Bond (Protein Donor)	false
CE	CB	SER- 47	3.88	0	Hydrophobic	false
C5'	CB	PRO- 49	3.91	0	Hydrophobic	false
CB	CA	ALA- 218	4.33	0	Hydrophobic	false
CB	CG	PRO- 219	3.54	0	Hydrophobic	false
CE	CG	PRO- 219	3.41	0	Hydrophobic	false
CG	CB	PHE- 243	4.24	0	Hydrophobic	false
C1'	CD2	PHE- 243	4.03	0	Hydrophobic	false
C4'	CB	PHE- 243	3.42	0	Hydrophobic	false
O	OG1	THR- 246	3.12	154.09	H-Bond (Protein Donor)	false
OXT	OG1	THR- 246	3.23	142.57	H-Bond (Protein Donor)	false
OXT	N	THR- 248	3.23	152.4	H-Bond (Protein Donor)	false
O3'	OE2	GLU- 264	3.49	120.79	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 264	2.78	169.37	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 264	2.93	142.76	H-Bond (Ligand Donor)	false
O2'	OE1	GLU- 264	3.35	154.49	H-Bond (Ligand Donor)	false
N3	N	LEU- 265	3.3	137.88	H-Bond (Protein Donor)	false
N	O	HOH- 311	3.17	131.69	H-Bond (Ligand Donor)	false