scPDB - 1ykg entry

Protein Data Bank Entry:

PDB ID : 1ykg

Resolution : Å

Experimental Method : NMR

Deposition Date : 2005-01-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Sulfite reductase [NADPH] flavoprotein alpha-component
ID:	CYSJ_ECOLI
AC:	P38038
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	0.000
Number of residues:	32
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.246	337.500

% Hydrophobic	% Polar
42.00	58.00
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	63.47 %
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
7.61768	13.8966	0.365548

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
C8M	CG	GLN- 70	4.43	0	Hydrophobic	false
O1P	N	GLN- 70	2.76	163.03	H-Bond (Protein Donor)	false
O5'	OG1	THR- 71	3.46	137.86	H-Bond (Protein Donor)	false
O1P	N	THR- 71	3.38	161.36	H-Bond (Protein Donor)	false
O2P	OG1	THR- 71	2.66	147.56	H-Bond (Protein Donor)	false
O2P	N	THR- 71	3.16	134.67	H-Bond (Protein Donor)	false
O2P	N	GLY- 72	2.8	177.45	H-Bond (Protein Donor)	false
O5'	ND2	ASN- 73	3.11	158.92	H-Bond (Protein Donor)	false
O2P	N	ASN- 73	2.72	158.71	H-Bond (Protein Donor)	false
O3P	N	ALA- 74	3.32	143.23	H-Bond (Protein Donor)	false
C5'	CB	SER- 116	3.9	0	Hydrophobic	false
O3'	O	LEU- 152	3.27	129.63	H-Bond (Ligand Donor)	false
C5'	CB	LEU- 152	3.79	0	Hydrophobic	false
N1	N	ASP- 154	3.38	120.33	H-Bond (Protein Donor)	false
O2	N	ASP- 154	2.79	156.73	H-Bond (Protein Donor)	false
C2'	CB	ASP- 154	4.37	0	Hydrophobic	false
N3	O	PHE- 159	2.8	148.91	H-Bond (Ligand Donor)	false
O2	N	CYS- 161	2.79	170.48	H-Bond (Protein Donor)	false