scPDB - 4k0b entry

Protein Data Bank Entry:

PDB ID : 4k0b

Resolution :2.390 Å

Experimental Method : X-ray

Deposition Date : 2013-04-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	S-adenosylmethionine synthase
ID:	METK_SULSO
AC:	Q980S9
Organism:	Sulfolobus solfataricus
Reign:	Archaea
TaxID:	273057
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	47 %
B	53 %

Ligand binding site composition:

B-Factor:	27.312
Number of residues:	51
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	2
Water Molecules:	4
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.087	344.250

% Hydrophobic	% Polar
48.04	51.96
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	71.29 %
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
29.3733	51.0239	6.51144

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
OXT	NE2	HIS- 58	2.7	147.66	H-Bond (Protein Donor)	false
O	ND2	ASN- 60	2.87	150.69	H-Bond (Protein Donor)	false
OXT	ND2	ASN- 60	3.3	120.17	H-Bond (Protein Donor)	false
N6	OD2	ASP- 144	2.8	138.25	H-Bond (Ligand Donor)	false
CB	CD1	LEU- 145	4.16	0	Hydrophobic	false
SD	CD1	LEU- 145	3.92	0	Hydrophobic	false
CE	CD2	LEU- 145	3.72	0	Hydrophobic	false
OXT	ND2	ASN- 159	3.37	159.89	H-Bond (Protein Donor)	false
CE	CB	ASP- 160	4.21	0	Hydrophobic	false
O2'	OD1	ASP- 199	2.66	131.32	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 199	3.29	161.14	H-Bond (Ligand Donor)	false
C1'	CB	ALA- 216	4.27	0	Hydrophobic	false
O2'	OH	TYR- 270	3.5	135.87	H-Bond (Protein Donor)	false
DuAr	DuAr	TYR- 270	3.91	0	Aromatic Face/Face	false
C2'	CZ	TYR- 270	4.29	0	Hydrophobic	false
C2'	CB	SER- 277	3.89	0	Hydrophobic	false
N	OD1	ASP- 282	2.65	146.73	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 282	3	154.2	H-Bond (Ligand Donor)	false
N	OD1	ASP- 282	2.65	0	Ionic (Ligand Cationic)	false
SD	CB	ASP- 282	4.09	0	Hydrophobic	false
C3'	CB	ASP- 282	4.08	0	Hydrophobic	false
CE	CD1	ILE- 349	4.48	0	Hydrophobic	false