scPDB - 1y56 entry

Protein Data Bank Entry:

PDB ID : 1y56

Resolution :2.860 Å

Experimental Method : X-ray

Deposition Date : 2004-12-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uncharacterized protein	382aa long hypothetical sarcosine oxidase
ID:	O59088_PYRHO	O59089_PYRHO
AC:	O59088	O59089
Organism:	Pyrococcus horikoshii
Reign:	Archaea
TaxID:	70601
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	33 %
B	67 %

Ligand binding site composition:

B-Factor:	33.801
Number of residues:	37
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.849	550.125

% Hydrophobic	% Polar
55.21	44.79
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	63.5 %
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
112.383	59.5292	24.5354

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
C5'	CG	ARG- 46	4.35	0	Hydrophobic	false
O1P	NH2	ARG- 46	3.01	139.66	H-Bond (Protein Donor)	false
O1P	NH1	ARG- 46	3.18	133.73	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 46	3.51	0	Ionic (Protein Cationic)	false
C8	CD1	ILE- 261	4.12	0	Hydrophobic	false
C7	CD1	ILE- 261	3.7	0	Hydrophobic	false
O4'	NH2	ARG- 302	3.2	151.91	H-Bond (Protein Donor)	false
C1'	CD	ARG- 302	4	0	Hydrophobic	false
C8M	CZ2	TRP- 304	3.81	0	Hydrophobic	false
C1'	CE3	TRP- 304	3.47	0	Hydrophobic	false
C3'	CD2	TRP- 304	4.37	0	Hydrophobic	false
C5'	CB	TRP- 304	4.16	0	Hydrophobic	false
C9	CZ2	TRP- 304	3.29	0	Hydrophobic	false
O2'	NZ	LYS- 437	3.4	128.93	H-Bond (Protein Donor)	false
O3'	NH1	ARG- 438	2.95	129.47	H-Bond (Protein Donor)	false
N3	O	MET- 444	3.38	156.24	H-Bond (Ligand Donor)	false
O2	NE2	GLN- 448	3.26	176.65	H-Bond (Protein Donor)	false
O1P	NE	ARG- 477	3.48	167.28	H-Bond (Protein Donor)	false
O5'	O	HOH- 808	3.21	179.96	H-Bond (Protein Donor)	false