scPDB - 3k7m entry

Protein Data Bank Entry:

PDB ID : 3k7m

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2009-10-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	6-hydroxy-L-nicotine oxidase
ID:	Q93NH4_ARTNI
AC:	Q93NH4
Organism:	Arthrobacter nicotinovorans
Reign:	Bacteria
TaxID:	29320
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	27.698
Number of residues:	67
Including
Standard Amino Acids:	62
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.055	546.750

% Hydrophobic	% Polar
54.32	45.68
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	76.14 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-37.3916	27.5452	62.3952

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
O1P	N	SER- 12	2.96	157.03	H-Bond (Protein Donor)	false
O3B	OE2	GLU- 31	3.22	121.48	H-Bond (Ligand Donor)	false
O3B	OE1	GLU- 31	2.73	175.72	H-Bond (Ligand Donor)	false
O2B	OE2	GLU- 31	2.64	157.06	H-Bond (Ligand Donor)	false
N3A	N	GLY- 32	3.04	136.22	H-Bond (Protein Donor)	false
O1A	N	ARG- 39	2.88	161.76	H-Bond (Protein Donor)	false
O2A	NE	ARG- 39	2.84	158.26	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 39	3.14	138.36	H-Bond (Protein Donor)	false
O3P	NH2	ARG- 39	3.3	147.71	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 39	3.43	0	Ionic (Protein Cationic)	false
C8M	CG	ARG- 39	3.87	0	Hydrophobic	false
C9	CB	ARG- 39	4.3	0	Hydrophobic	false
C3'	CB	ARG- 39	3.99	0	Hydrophobic	false
N3	O	TYR- 59	2.85	158.69	H-Bond (Ligand Donor)	false
O4	N	TYR- 59	3.19	134.32	H-Bond (Protein Donor)	false
N6A	O	VAL- 226	3.03	165.87	H-Bond (Ligand Donor)	false
N1A	N	VAL- 226	2.9	158.4	H-Bond (Protein Donor)	false
C1B	CG2	THR- 255	4.3	0	Hydrophobic	false
C5B	CG	PRO- 256	3.87	0	Hydrophobic	false
C6	CD	LYS- 287	4.28	0	Hydrophobic	false
C7M	CB	LYS- 287	3.8	0	Hydrophobic	false
C8M	CE2	TRP- 361	3.9	0	Hydrophobic	false
C2B	CB	LEU- 366	4.24	0	Hydrophobic	false
C2B	CE1	PHE- 367	3.84	0	Hydrophobic	false
C8M	CB	PRO- 370	3.86	0	Hydrophobic	false
C7M	CZ3	TRP- 371	3.74	0	Hydrophobic	false
C8M	CE3	TRP- 371	4.32	0	Hydrophobic	false
C9	CB	TRP- 371	4.19	0	Hydrophobic	false
C1'	CB	TRP- 371	3.94	0	Hydrophobic	false
O3'	OG	SER- 398	2.84	161.92	H-Bond (Ligand Donor)	false
O2P	N	SER- 398	2.91	142.15	H-Bond (Protein Donor)	false
C5'	CB	SER- 398	3.91	0	Hydrophobic	false
N1	N	ILE- 408	3.44	146.37	H-Bond (Protein Donor)	false
O2	N	ILE- 408	2.76	152.98	H-Bond (Protein Donor)	false
C2'	CG1	ILE- 408	4.22	0	Hydrophobic	false
O3'	O	HOH- 448	3.01	153.97	H-Bond (Protein Donor)	false
O3B	O	HOH- 476	2.6	168.67	H-Bond (Protein Donor)	false
O1P	O	HOH- 611	2.89	179.95	H-Bond (Protein Donor)	false