scPDB - 2byc entry

Protein Data Bank Entry:

PDB ID : 2byc

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2005-07-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Blue-light receptor of the BLUF-family
ID:	Q3IYE4_RHOS4
AC:	Q3IYE4
Organism:	Rhodobacter sphaeroides
Reign:	Bacteria
TaxID:	272943
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	21.192
Number of residues:	30
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.288	317.250

% Hydrophobic	% Polar
57.45	42.55
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	62.05 %
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
11.693	30.6927	-11.6941

Binding mode :

What is Poseview ?

2D View
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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
C6	CG2	ILE- 525	4.19	0	Hydrophobic	false
C9	CG1	ILE- 525	3.63	0	Hydrophobic	false
C9A	CG2	ILE- 525	3.78	0	Hydrophobic	false
C1'	CG1	ILE- 525	4.37	0	Hydrophobic	false
C8	CD1	ILE- 525	3.57	0	Hydrophobic	false
C4'	CB	ALA- 528	3.82	0	Hydrophobic	false
N3	OD1	ASN- 533	2.76	175.88	H-Bond (Ligand Donor)	false
O4	ND2	ASN- 533	3.28	161.47	H-Bond (Protein Donor)	false
C6	CD2	LEU- 542	4.28	0	Hydrophobic	false
C7M	CD1	LEU- 542	4.16	0	Hydrophobic	false
C7M	CD1	PHE- 549	3.32	0	Hydrophobic	false
C8M	CE1	PHE- 549	4.16	0	Hydrophobic	false
O4	NE2	GLN- 551	2.93	130.77	H-Bond (Protein Donor)	false
N5	NE2	GLN- 551	3.2	150.04	H-Bond (Protein Donor)	false
C3'	CD1	LEU- 566	4.31	0	Hydrophobic	false
C9A	CG1	ILE- 567	4.23	0	Hydrophobic	false
C6	CG2	ILE- 567	4.09	0	Hydrophobic	false
C8M	CB	ASP- 570	4.28	0	Hydrophobic	false
C9	CB	ASP- 570	4.42	0	Hydrophobic	false
O2'	OD2	ASP- 570	2.7	168.05	H-Bond (Ligand Donor)	false
C8M	CB	ARG- 572	4.12	0	Hydrophobic	false