scPDB - 4rv9 entry

Protein Data Bank Entry:

PDB ID : 4rv9

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2014-11-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	D-mycarose 3-C-methyltransferase
ID:	Q194Q4_STRAA
AC:	Q194Q4
Organism:	Streptomyces argillaceus
Reign:	Bacteria
TaxID:	41951
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	50.907
Number of residues:	32
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	CL

Cavity properties

Ligandability	Volume (Å3)
0.847	1650.375

% Hydrophobic	% Polar
47.24	52.76
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	66.58 %
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
-30.939	2.67823	3.89835

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
C5'	CE1	TYR- 74	4.32	0	Hydrophobic	false
C2'	CD1	TYR- 74	3.86	0	Hydrophobic	false
C5'	CE2	TYR- 77	4.18	0	Hydrophobic	false
C3'	CD2	TYR- 77	3.83	0	Hydrophobic	false
N	O	GLY- 114	2.91	169.13	H-Bond (Ligand Donor)	false
O3'	ND2	ASN- 116	2.88	152.47	H-Bond (Protein Donor)	false
O3'	OD1	ASP- 135	2.52	153.01	H-Bond (Ligand Donor)	false
C1'	CG	PRO- 136	4.25	0	Hydrophobic	false
N1	N	PHE- 156	3.09	171.84	H-Bond (Protein Donor)	false
N	O	ARG- 177	2.88	143.46	H-Bond (Ligand Donor)	false
CB	CB	HIS- 178	4.08	0	Hydrophobic	false
SD	CB	VAL- 179	4.45	0	Hydrophobic	false
C1'	CG2	VAL- 179	4.29	0	Hydrophobic	false