scPDB - 3mkh entry

Protein Data Bank Entry:

PDB ID : 3mkh

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2010-04-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Nitroalkane oxidase
ID:	B2AM55_PODAN
AC:	B2AM55
Organism:	Podospora anserina
Reign:	Eukaryota
TaxID:	515849
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	67 %
B	31 %
D	2 %

Ligand binding site composition:

B-Factor:	24.823
Number of residues:	65
Including
Standard Amino Acids:	61
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.626	1890.000

% Hydrophobic	% Polar
49.29	50.71
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	73.02 %
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
82.0498	43.3989	78.205

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
C6	CD2	LEU- 94	4.32	0	Hydrophobic	false
C7M	CD2	LEU- 94	3.83	0	Hydrophobic	false
N3	O	LEU- 132	2.7	150.82	H-Bond (Ligand Donor)	false
O2	N	PHE- 134	2.99	142.57	H-Bond (Protein Donor)	false
N1	OG	SER- 135	2.86	167.59	H-Bond (Protein Donor)	false
O2	N	SER- 135	2.83	160.61	H-Bond (Protein Donor)	false
C1'	CB	SER- 135	4.08	0	Hydrophobic	false
C4'	CB	SER- 135	4.22	0	Hydrophobic	false
O4'	OG	SER- 135	2.6	155.44	H-Bond (Ligand Donor)	false
O1A	N	VAL- 140	3.01	132.45	H-Bond (Protein Donor)	false
C5'	CG2	VAL- 140	4.19	0	Hydrophobic	false
O1A	N	ALA- 141	2.96	163.8	H-Bond (Protein Donor)	false
N7A	ND2	ASN- 142	3.15	143.67	H-Bond (Protein Donor)	false
N6A	OD1	ASN- 142	2.78	164.33	H-Bond (Ligand Donor)	false
C8M	CE3	TRP- 170	3.48	0	Hydrophobic	false
C1'	CB	TRP- 170	3.47	0	Hydrophobic	false
C9	CB	TRP- 170	3.79	0	Hydrophobic	false
O4	N	THR- 172	3.36	141.83	H-Bond (Protein Donor)	false
N5	OG1	THR- 172	2.84	152.56	H-Bond (Protein Donor)	false
C6	CB	THR- 172	4.43	0	Hydrophobic	false
C7M	CG1	VAL- 238	4.39	0	Hydrophobic	false
O2A	NH1	ARG- 301	2.88	154.66	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 301	3.95	0	Ionic (Protein Cationic)	false
C5B	CD	ARG- 301	3.35	0	Hydrophobic	false
C1B	CD1	LEU- 307	3.65	0	Hydrophobic	false
N1A	NE2	GLN- 311	3.03	152.62	H-Bond (Protein Donor)	false
C1B	CD2	PHE- 313	4.26	0	Hydrophobic	false
O3B	O	ASN- 372	3.2	134.45	H-Bond (Ligand Donor)	false
O2B	O	ALA- 373	2.6	162	H-Bond (Ligand Donor)	false
C3'	CB	ILE- 376	3.81	0	Hydrophobic	false
C1'	CG1	ILE- 376	4.12	0	Hydrophobic	false
C4'	CG2	ILE- 376	4.24	0	Hydrophobic	false
C8M	CD1	ILE- 376	3.25	0	Hydrophobic	false
O2P	N	ILE- 376	2.96	164.51	H-Bond (Protein Donor)	false
C8M	CD2	TYR- 379	3.68	0	Hydrophobic	false
C7M	CG2	VAL- 394	4.33	0	Hydrophobic	false
C8M	CG2	VAL- 394	3.65	0	Hydrophobic	false
O3'	O	ILE- 397	2.81	158.05	H-Bond (Ligand Donor)	false
C7M	CD2	PHE- 398	4.11	0	Hydrophobic	false
C2'	CB	PHE- 398	4.04	0	Hydrophobic	false
C9	CB	PHE- 398	3.9	0	Hydrophobic	false
O3'	N	GLY- 400	2.98	135.8	H-Bond (Protein Donor)	false
O1P	N	GLY- 401	2.71	135.45	H-Bond (Protein Donor)	false
C2B	CG1	VAL- 403	3.93	0	Hydrophobic	false
C5'	CD1	ILE- 405	4.1	0	Hydrophobic	false
O2A	O	HOH- 456	2.85	179.97	H-Bond (Protein Donor)	false
O4	O	HOH- 495	2.64	163.72	H-Bond (Protein Donor)	false