scPDB - 1skm entry

Protein Data Bank Entry:

PDB ID : 1skm

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2004-03-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Modification methylase HhaI
ID:	MTH1_HAEPH
AC:	P05102
Organism:	Haemophilus parahaemolyticus
Reign:	Bacteria
TaxID:	735
EC Number:	2.1.1.37

Chains:

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

Ligand binding site composition:

B-Factor:	21.923
Number of residues:	43
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.687	570.375

% Hydrophobic	% Polar
44.38	55.62
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	71.88 %
Polar Surface area:	212.38 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-17.7287	83.8894	190.515

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'	CD1	PHE- 18	4.15	0	Hydrophobic	false
C4'	CB	PHE- 18	3.88	0	Hydrophobic	false
OXT	N	LEU- 21	2.92	152.77	H-Bond (Protein Donor)	false
O	N	GLY- 23	2.91	143.17	H-Bond (Protein Donor)	false
O3'	OE1	GLU- 40	2.77	170.17	H-Bond (Ligand Donor)	false
O3'	OE2	GLU- 40	3.28	131.36	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 40	2.69	151.12	H-Bond (Ligand Donor)	false
N3	N	TRP- 41	3.19	144.72	H-Bond (Protein Donor)	false
N6	OD1	ASP- 60	3.23	154.31	H-Bond (Ligand Donor)	false
N1	N	ILE- 61	2.99	172.09	H-Bond (Protein Donor)	false
C5'	CG	PRO- 80	4.21	0	Hydrophobic	false
CB	CB	ASN- 304	4.5	0	Hydrophobic	false
SD	CB	ASN- 304	3.77	0	Hydrophobic	false
O	OG	SER- 305	3.41	142.61	H-Bond (Protein Donor)	false
OXT	OG	SER- 305	2.92	158.45	H-Bond (Protein Donor)	false
N	O	HOH- 338	2.59	137.64	H-Bond (Ligand Donor)	false