scPDB - 2yvg entry

Protein Data Bank Entry:

PDB ID : 2yvg

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2007-04-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ferredoxin reductase
ID:	Q52437_PSES1
AC:	Q52437
Organism:	Pseudomonas sp.
Reign:	Bacteria
TaxID:	307
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	27.586
Number of residues:	53
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	1
Water Molecules:	6
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.506	492.750

% Hydrophobic	% Polar
39.73	60.27
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	69.82 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
72.7981	22.148	10.3387

Binding mode :

What is Poseview ?

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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
N7A	NH2	ARG- 114	3.23	130.32	H-Bond (Protein Donor)	false
C2D	CG2	VAL- 155	3.85	0	Hydrophobic	false
C3N	CG2	VAL- 155	3.3	0	Hydrophobic	false
C4N	CB	VAL- 155	3.52	0	Hydrophobic	false
C5N	CG2	VAL- 155	3.79	0	Hydrophobic	false
O1N	N	ILE- 156	2.97	154.15	H-Bond (Protein Donor)	false
C5D	CG1	ILE- 156	3.96	0	Hydrophobic	false
C5N	CG1	ILE- 156	3.59	0	Hydrophobic	false
N7N	OE2	GLU- 159	2.58	165.28	H-Bond (Ligand Donor)	false
O3B	OE2	GLU- 175	2.85	134.76	H-Bond (Ligand Donor)	false
O2B	OE1	GLU- 175	2.78	168.42	H-Bond (Ligand Donor)	false
O1A	CZ	ARG- 183	3.78	0	Ionic (Protein Cationic)	false
O2A	CZ	ARG- 183	3.39	0	Ionic (Protein Cationic)	false
O1A	NE	ARG- 183	2.85	158.82	H-Bond (Protein Donor)	false
O2A	NE	ARG- 183	3.28	130.76	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 183	2.66	157.17	H-Bond (Protein Donor)	false
O2N	N	GLY- 236	2.98	146.65	H-Bond (Protein Donor)	false
C5D	CG1	VAL- 237	3.72	0	Hydrophobic	false
C3D	CG	GLU- 289	4.46	0	Hydrophobic	false
O3D	OE2	GLU- 289	2.52	161.42	H-Bond (Ligand Donor)	false
O2D	O	GLU- 289	2.89	138.99	H-Bond (Ligand Donor)	false
N7N	O	TRP- 320	2.68	153.41	H-Bond (Ligand Donor)	false
C5N	C7M	FAD- 1449	4.47	0	Hydrophobic	false
O1N	O	HOH- 1582	2.7	179.94	H-Bond (Protein Donor)	false
O1A	O	HOH- 1586	2.87	179.97	H-Bond (Protein Donor)	false
O3B	O	HOH- 1655	2.68	131.33	H-Bond (Protein Donor)	false
O3D	O	HOH- 1708	2.79	179.96	H-Bond (Protein Donor)	false