scPDB - 3b9o entry

Protein Data Bank Entry:

PDB ID : 3b9o

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2007-11-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Alkane monoxygenase
ID:	A4IU28_GEOTN
AC:	A4IU28
Organism:	Geobacillus thermodenitrificans
Reign:	Bacteria
TaxID:	420246
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	25.581
Number of residues:	40
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.319	1242.000

% Hydrophobic	% Polar
50.54	49.46
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	61.77 %
Polar Surface area:	217.05 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-25.7953	34.3678	19.4007

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
N3	O	ASP- 58	2.8	165.44	H-Bond (Ligand Donor)	false
O4	N	ASP- 58	3.45	155.19	H-Bond (Protein Donor)	false
C2'	CG2	VAL- 135	4.36	0	Hydrophobic	false
C3'	CG1	VAL- 135	4.42	0	Hydrophobic	false
O3'	N	SER- 137	3.1	136.51	H-Bond (Protein Donor)	false
O3'	ND1	HIS- 138	2.99	122.22	H-Bond (Protein Donor)	false
O1P	NE2	HIS- 154	2.86	152.37	H-Bond (Protein Donor)	false
O5'	OH	TYR- 158	3.19	153.24	H-Bond (Protein Donor)	false
O2P	OH	TYR- 158	2.64	132.94	H-Bond (Protein Donor)	false
C6	CB	ALA- 227	3.68	0	Hydrophobic	false
C8M	CG	MET- 229	3.53	0	Hydrophobic	false
O3P	N	MET- 229	2.51	121.68	H-Bond (Protein Donor)	false
O2P	N	SER- 230	3.34	138.01	H-Bond (Protein Donor)	false
O3P	N	SER- 230	3	153.89	H-Bond (Protein Donor)	false
C7M	CD1	PHE- 245	3.62	0	Hydrophobic	false
C7M	CE1	PHE- 349	4.28	0	Hydrophobic	false
O2'	O	HOH- 575	3.16	143.46	H-Bond (Ligand Donor)	false