scPDB - 3r9f entry

Protein Data Bank Entry:

PDB ID : 3r9f

Resolution :1.200 Å

Experimental Method : X-ray

Deposition Date : 2011-03-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	MccE protein
ID:	Q47510_ECOLX
AC:	Q47510
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	562
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	11.368
Number of residues:	34
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:	COA
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.741	648.000

% Hydrophobic	% Polar
48.44	51.56
According to VolSite

Ligand :

HET Code:	GSU
Formula:	C15H20N7O9S
Molecular weight:	474.426 g/mol
DrugBank ID:	-
Buried Surface Area:	59.43 %
Polar Surface area:	269.99 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
65.3396	7.382	7.86978

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'	SD	MET- 46	3.92	0	Hydrophobic	false
O1S	NE1	TRP- 48	2.9	129.21	H-Bond (Protein Donor)	false
C1'	CZ2	TRP- 48	4.15	0	Hydrophobic	false
DuAr	DuAr	TRP- 48	3.49	0	Aromatic Face/Face	false
C1'	CG1	VAL- 88	4.19	0	Hydrophobic	false
O2'	OG	SER- 90	3.38	150.08	H-Bond (Ligand Donor)	false
O3'	OG	SER- 90	2.83	153.56	H-Bond (Ligand Donor)	false
C3'	CB	SER- 90	4.37	0	Hydrophobic	false
O	ND2	ASN- 92	2.62	131.72	H-Bond (Protein Donor)	false
N3	NE1	TRP- 106	3.09	166.62	H-Bond (Protein Donor)	false
N	O	LYS- 140	2.72	151.65	H-Bond (Ligand Donor)	false
OE1	NE2	GLN- 176	2.94	144.12	H-Bond (Protein Donor)	false
N10	O	HOH- 348	3.41	145.25	H-Bond (Ligand Donor)	false
CB	S1P	COA- 400	4.01	0	Hydrophobic	false