scPDB - 4yx6 entry

Protein Data Bank Entry:

PDB ID : 4yx6

Resolution :1.860 Å

Experimental Method : X-ray

Deposition Date : 2015-03-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Omega-3 polyunsaturated fatty acid synthase subunit PfaD
ID:	Q8EGK4_SHEON
AC:	Q8EGK4
Organism:	Shewanella oneidensis
Reign:	Bacteria
TaxID:	211586
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	98 %
B	2 %

Ligand binding site composition:

B-Factor:	9.659
Number of residues:	54
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	1
Water Molecules:	6
Cofactors:
Metals:	CA

Cavity properties

Ligandability	Volume (Å3)
1.243	1221.750

% Hydrophobic	% Polar
45.58	54.42
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	74.09 %
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
-12.2941	47.2183	-16.5921

Binding mode :

What is Poseview ?

2D View
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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
O2'	O	ALA- 108	2.67	156.84	H-Bond (Ligand Donor)	false
C6	CB	MET- 109	3.39	0	Hydrophobic	false
C9A	CG	MET- 109	4.06	0	Hydrophobic	false
N5	N	ALA- 110	2.85	149.12	H-Bond (Protein Donor)	false
C7M	CD1	ILE- 113	4.27	0	Hydrophobic	false
N3	OD1	ASN- 160	3.03	129.97	H-Bond (Ligand Donor)	false
O2	OG	SER- 189	2.69	137.95	H-Bond (Protein Donor)	false
N1	NZ	LYS- 223	3.05	152.49	H-Bond (Protein Donor)	false
O2	NZ	LYS- 223	3.3	133.87	H-Bond (Protein Donor)	false
O3'	NZ	LYS- 223	2.86	169.15	H-Bond (Protein Donor)	false
O3'	OE2	GLU- 271	2.93	161.44	H-Bond (Ligand Donor)	false
C4'	CB	SER- 274	4.03	0	Hydrophobic	false
O2P	N	GLY- 275	3	165.08	H-Bond (Protein Donor)	false
O3P	N	GLY- 314	2.78	177.62	H-Bond (Protein Donor)	false
C3'	CG1	VAL- 333	4.46	0	Hydrophobic	false
C8M	CB	SER- 336	4.46	0	Hydrophobic	false
O1P	N	SER- 336	3.1	170.43	H-Bond (Protein Donor)	false
O2P	N	SER- 336	3.33	124.21	H-Bond (Protein Donor)	false
O2P	OG	SER- 336	2.55	159.48	H-Bond (Protein Donor)	false
C7M	CB	TRP- 482	3.41	0	Hydrophobic	false
O1P	O	HOH- 741	2.69	153.54	H-Bond (Protein Donor)	false
O4	O	HOH- 748	2.76	147.1	H-Bond (Protein Donor)	false
O1P	O	HOH- 773	2.77	158.51	H-Bond (Protein Donor)	false