scPDB - 2yvj entry

Protein Data Bank Entry:

PDB ID : 2yvj

Resolution :1.900 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:	36.133
Number of residues:	53
Including
Standard Amino Acids:	51
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:	NAI
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.066	1093.500

% Hydrophobic	% Polar
44.75	55.25
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	71.36 %
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
7.91536	-21.5422	17.0245

Binding mode :

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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
O1P	N	ALA- 18	3.13	172.26	H-Bond (Protein Donor)	false
O2B	OD2	ASP- 40	2.53	155.15	H-Bond (Ligand Donor)	false
N3A	N	ASP- 40	2.92	128.43	H-Bond (Protein Donor)	false
O2B	OE1	GLU- 41	3.08	172.73	H-Bond (Protein Donor)	false
C3B	CG	GLU- 41	4.21	0	Hydrophobic	false
O1A	CZ	ARG- 48	3.31	0	Ionic (Protein Cationic)	false
O2A	CZ	ARG- 48	3.33	0	Ionic (Protein Cationic)	false
C8M	CD	ARG- 48	3.98	0	Hydrophobic	false
C9	CB	ARG- 48	4.17	0	Hydrophobic	false
C9A	CG	PRO- 49	4.31	0	Hydrophobic	false
C7M	CB	LEU- 51	4.35	0	Hydrophobic	false
C6	CB	SER- 52	4.22	0	Hydrophobic	false
C7M	CB	SER- 52	4.23	0	Hydrophobic	false
N6A	O	ALA- 82	3.07	175.3	H-Bond (Ligand Donor)	false
N1A	N	ALA- 82	3.11	173.15	H-Bond (Protein Donor)	false
C7M	CG	LEU- 129	4.26	0	Hydrophobic	false
O1A	NH1	ARG- 130	3.14	172.26	H-Bond (Protein Donor)	false
C8M	CG	ARG- 130	3.83	0	Hydrophobic	false
C7M	CD1	ILE- 156	3.99	0	Hydrophobic	false
O3'	OD1	ASP- 273	2.97	161.44	H-Bond (Ligand Donor)	false
C5'	CB	ASP- 273	4.37	0	Hydrophobic	false
O2P	N	ASP- 273	2.95	152.08	H-Bond (Protein Donor)	false
N1	N	TRP- 291	3.18	140.01	H-Bond (Protein Donor)	false
O2	N	TRP- 291	2.86	154.76	H-Bond (Protein Donor)	false
C2'	CB	TRP- 291	4.49	0	Hydrophobic	false
C5'	CB	ALA- 294	3.61	0	Hydrophobic	false
C1'	C1D	NAI- 503	4.06	0	Hydrophobic	false
C9A	C1D	NAI- 503	4.12	0	Hydrophobic	false