scPDB - 5dbj entry

Protein Data Bank Entry:

PDB ID : 5dbj

Resolution :2.750 Å

Experimental Method : X-ray

Deposition Date : 2015-08-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	FADH2-dependent halogenase PltA
ID:	Q4KCZ0_PSEF5
AC:	Q4KCZ0
Organism:	Pseudomonas fluorescens
Reign:	Bacteria
TaxID:	220664
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	56.010
Number of residues:	68
Including
Standard Amino Acids:	65
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	CL

Cavity properties

Ligandability	Volume (Å3)
0.730	884.250

% Hydrophobic	% Polar
48.09	51.91
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	80.67 %
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
29.8668	-41.0787	2.16679

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
O2P	N	ALA- 16	2.86	168.02	H-Bond (Protein Donor)	false
O3B	OE1	GLU- 35	2.65	165.8	H-Bond (Ligand Donor)	false
O3B	OE2	GLU- 35	3.04	129.05	H-Bond (Ligand Donor)	false
O2B	OE1	GLU- 35	3.5	139.52	H-Bond (Ligand Donor)	false
O2B	OE2	GLU- 35	2.59	164.74	H-Bond (Ligand Donor)	false
N3A	N	LYS- 36	3.12	145.5	H-Bond (Protein Donor)	false
C2B	CG	LYS- 36	4.26	0	Hydrophobic	false
O3B	NH1	ARG- 41	2.65	139.74	H-Bond (Protein Donor)	false
O1A	NE2	HIS- 43	2.86	135.36	H-Bond (Protein Donor)	false
C6	CG2	VAL- 44	3.87	0	Hydrophobic	false
C7M	CG2	VAL- 44	4.04	0	Hydrophobic	false
C8M	CG1	VAL- 44	3.77	0	Hydrophobic	false
C8	CG1	VAL- 44	3.49	0	Hydrophobic	false
N3	O	SER- 47	2.59	160.17	H-Bond (Ligand Donor)	false
O2A	NH2	ARG- 123	2.89	127.73	H-Bond (Protein Donor)	false
O2'	NH1	ARG- 123	3.12	138.96	H-Bond (Protein Donor)	false
O4'	NH2	ARG- 123	2.92	147.29	H-Bond (Protein Donor)	false
O4'	NH1	ARG- 123	3.12	137.82	H-Bond (Protein Donor)	false
N6A	O	ILE- 147	2.77	178.9	H-Bond (Ligand Donor)	false
N1A	N	ILE- 147	2.83	165.87	H-Bond (Protein Donor)	false
N7A	OG	SER- 180	3.44	155.69	H-Bond (Protein Donor)	false
C8M	CD	ARG- 182	4.36	0	Hydrophobic	false
C7M	CB	ALA- 203	3.48	0	Hydrophobic	false
C7M	CZ3	TRP- 239	3.78	0	Hydrophobic	false
C7M	CG	GLU- 296	4.02	0	Hydrophobic	false
C8M	CB	GLU- 296	4.12	0	Hydrophobic	false
C7M	CE2	TYR- 299	4.41	0	Hydrophobic	false
C8M	CD2	TYR- 299	3.82	0	Hydrophobic	false
O3'	OD1	ASP- 316	2.5	161.86	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 316	2.96	123.75	H-Bond (Ligand Donor)	false
O1P	N	ASP- 316	2.95	143.21	H-Bond (Protein Donor)	false
C8M	CE2	PHE- 320	4.14	0	Hydrophobic	false
C1'	CE1	PHE- 320	3.69	0	Hydrophobic	false
C6	CG	PRO- 323	3.43	0	Hydrophobic	false
C9A	CB	PRO- 323	3.69	0	Hydrophobic	false
O2	N	VAL- 329	3.15	159.83	H-Bond (Protein Donor)	false
C2'	CG2	VAL- 329	4.25	0	Hydrophobic	false
C4'	CG2	VAL- 329	4.02	0	Hydrophobic	false
C5'	CB	ALA- 332	3.77	0	Hydrophobic	false
O2P	O	HOH- 603	3.1	179.99	H-Bond (Protein Donor)	false