scPDB - 2gj3 entry

Protein Data Bank Entry:

PDB ID : 2gj3

Resolution :1.040 Å

Experimental Method : X-ray

Deposition Date : 2006-03-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Nitrogen fixation regulatory protein
ID:	NIFL_AZOVI
AC:	P30663
Organism:	Azotobacter vinelandii
Reign:	Bacteria
TaxID:	354
EC Number:	2.7.13.3

Chains:

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

Ligand binding site composition:

B-Factor:	14.028
Number of residues:	40
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.994	371.250

% Hydrophobic	% Polar
64.55	35.45
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	57.19 %
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
32.4662	2.01562	47.508

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
C7M	CG2	THR- 41	3.89	0	Hydrophobic	false
C8M	CB	ALA- 45	3.79	0	Hydrophobic	false
O2B	OD1	ASN- 69	2.73	147.37	H-Bond (Ligand Donor)	false
C6	CG	GLU- 70	3.6	0	Hydrophobic	false
C9A	CB	GLU- 70	3.55	0	Hydrophobic	false
C2'	CB	GLU- 70	4.03	0	Hydrophobic	false
C3'	CB	SER- 71	4.34	0	Hydrophobic	false
C3B	CB	SER- 71	3.93	0	Hydrophobic	false
C5'	CB	SER- 74	3.87	0	Hydrophobic	false
O2A	NH2	ARG- 80	3.25	124.1	H-Bond (Protein Donor)	false
O2P	NH2	ARG- 80	2.84	145.77	H-Bond (Protein Donor)	false
O2P	NH1	ARG- 80	2.8	145.73	H-Bond (Protein Donor)	false
O2P	CZ	ARG- 80	3.26	0	Ionic (Protein Cationic)	false
C4'	CD2	TYR- 83	3.62	0	Hydrophobic	false
C5'	CD1	TYR- 83	3.62	0	Hydrophobic	false
C9	CD2	LEU- 86	4.01	0	Hydrophobic	false
C9A	CD1	LEU- 86	4.31	0	Hydrophobic	false
C1'	CD1	LEU- 86	4.12	0	Hydrophobic	false
C1B	CZ2	TRP- 87	4.33	0	Hydrophobic	false
C8M	CZ2	TRP- 87	3.94	0	Hydrophobic	false
O2'	NE1	TRP- 87	3.26	139.57	H-Bond (Protein Donor)	false
O3'	NE1	TRP- 87	2.88	142.15	H-Bond (Protein Donor)	false
DuAr	DuAr	TRP- 87	3.84	0	Aromatic Face/Face	false
C8M	CD1	LEU- 90	3.76	0	Hydrophobic	false
N3	OD1	ASN- 102	2.78	171.68	H-Bond (Ligand Donor)	false
O4	ND2	ASN- 102	2.99	151.72	H-Bond (Protein Donor)	false
C6	CG1	VAL- 116	3.56	0	Hydrophobic	false
C7M	CB	TYR- 129	3.7	0	Hydrophobic	false
C8M	CB	TYR- 129	3.77	0	Hydrophobic	false