scPDB - 1jra entry

Protein Data Bank Entry:

PDB ID : 1jra

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2001-08-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	FAD-linked sulfhydryl oxidase ERV2
ID:	ERV2_YEAST
AC:	Q12284
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	1.8.3.2

Chains:

Chain Name:	Percentage of Residues within binding site
B	9 %
D	91 %

Ligand binding site composition:

B-Factor:	24.408
Number of residues:	46
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.986	1491.750

% Hydrophobic	% Polar
50.90	49.10
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	66.28 %
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
25.5766	22.2278	13.4201

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
O2	NZ	LYS- 11	2.97	129.71	H-Bond (Protein Donor)	false
C4'	CG	LYS- 12	4.07	0	Hydrophobic	false
C5'	CB	LYS- 12	4.03	0	Hydrophobic	false
C5'	CG	ARG- 16	4	0	Hydrophobic	false
O2P	CZ	ARG- 16	3.64	0	Ionic (Protein Cationic)	false
O2P	NE	ARG- 16	2.7	153.42	H-Bond (Protein Donor)	false
C8M	CB	SER- 18	3.49	0	Hydrophobic	false
C5B	CB	TRP- 19	4.1	0	Hydrophobic	false
C7M	CH2	TRP- 19	4.06	0	Hydrophobic	false
C8M	CE2	TRP- 19	3.43	0	Hydrophobic	false
O2'	NE1	TRP- 19	2.93	173.01	H-Bond (Protein Donor)	false
C7M	CE2	TYR- 48	3.68	0	Hydrophobic	false
C7M	CD1	TYR- 52	4.1	0	Hydrophobic	false
C8M	CE1	TYR- 52	3.48	0	Hydrophobic	false
C6	CB	CYS- 57	4.11	0	Hydrophobic	false
C9A	CB	CYS- 57	4.37	0	Hydrophobic	false
C6	CB	PHE- 61	4.38	0	Hydrophobic	false
C7M	CG	PHE- 61	3.62	0	Hydrophobic	false
N6A	O	CYS- 83	3.07	163.08	H-Bond (Ligand Donor)	false
O1A	NE2	HIS- 86	2.82	165.6	H-Bond (Protein Donor)	false
N6A	OD1	ASN- 87	3.12	122.52	H-Bond (Ligand Donor)	false
N7A	ND2	ASN- 90	3.04	160.57	H-Bond (Protein Donor)	false
C2'	CD1	LEU- 93	3.96	0	Hydrophobic	false
O1P	NZ	LYS- 95	3.11	155.18	H-Bond (Protein Donor)	false
O1P	NZ	LYS- 95	3.11	0	Ionic (Protein Cationic)	false
DuAr	DuAr	TYR- 98	3.79	0	Aromatic Face/Face	false
C1B	CE1	TYR- 98	4.02	0	Hydrophobic	false
N3A	OH	TYR- 107	2.71	150.32	H-Bond (Protein Donor)	false