scPDB - 5jdz entry

Protein Data Bank Entry:

PDB ID : 5jdz

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2016-04-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Methyl transferase
ID:	Q9LBJ0_BURGL
AC:	Q9LBJ0
Organism:	Burkholderia glumae
Reign:	Bacteria
TaxID:	337
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	19.477
Number of residues:	34
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.509	550.125

% Hydrophobic	% Polar
50.92	49.08
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	62.74 %
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
24.6383	37.4427	40.1067

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
O	NH2	ARG- 24	2.89	166.94	H-Bond (Protein Donor)	false
OXT	NH1	ARG- 24	3.12	164.9	H-Bond (Protein Donor)	false
O	CZ	ARG- 24	3.84	0	Ionic (Protein Cationic)	false
OXT	CZ	ARG- 24	3.8	0	Ionic (Protein Cationic)	false
N	O	ALA- 47	2.74	157.51	H-Bond (Ligand Donor)	false
C4'	CB	ALA- 47	3.98	0	Hydrophobic	false
C1'	CB	ALA- 47	3.88	0	Hydrophobic	false
O3'	OD2	ASP- 69	2.64	172.43	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 69	3.42	126.02	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 69	2.65	156.64	H-Bond (Ligand Donor)	false
C1'	CG2	ILE- 70	4.46	0	Hydrophobic	false
N3	N	ILE- 70	3.16	142.99	H-Bond (Protein Donor)	false
N6	OD1	ASP- 95	2.93	143.01	H-Bond (Ligand Donor)	false
N1	N	VAL- 96	2.98	179.36	H-Bond (Protein Donor)	false
N	O	ALA- 111	2.78	147.33	H-Bond (Ligand Donor)	false
C5'	CB	TRP- 112	4.35	0	Hydrophobic	false
CG	CB	TRP- 112	3.79	0	Hydrophobic	false
C5'	CE2	TYR- 116	3.45	0	Hydrophobic	false
N	O	HOH- 462	3.28	124.33	H-Bond (Ligand Donor)	false
OXT	O	HOH- 553	2.98	179.96	H-Bond (Protein Donor)	false