scPDB - 3kyb entry

Protein Data Bank Entry:

PDB ID : 3kyb

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2009-12-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	UDP-galactopyranose mutase
ID:	GLF1_KLEPN
AC:	Q48485
Organism:	Klebsiella pneumoniae
Reign:	Bacteria
TaxID:	573
EC Number:	5.4.99.9

Chains:

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

Ligand binding site composition:

B-Factor:	30.215
Number of residues:	26
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.624	1086.750

% Hydrophobic	% Polar
42.24	57.76
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	47.37 %
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
45.4081	29.3958	2.56019

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
C8M	CB	GLN- 159	4.02	0	Hydrophobic	false
C7M	CH2	TRP- 160	3.23	0	Hydrophobic	false
C8M	CE2	TRP- 160	4.09	0	Hydrophobic	false
C7	CZ2	TRP- 160	3.37	0	Hydrophobic	false
O2'	NH1	ARG- 174	3.27	130.67	H-Bond (Protein Donor)	false
C7M	CG	ARG- 250	4.32	0	Hydrophobic	false
C8M	CG	ARG- 250	4.4	0	Hydrophobic	false
C8M	CG	TYR- 314	3.73	0	Hydrophobic	false
C1'	CE2	TYR- 314	3.75	0	Hydrophobic	false
C9	CD2	TYR- 314	3.3	0	Hydrophobic	false
C7	CB	TYR- 314	3.31	0	Hydrophobic	false
C8	CB	TYR- 314	3.45	0	Hydrophobic	false
O4'	OH	TYR- 314	3.15	146.74	H-Bond (Ligand Donor)	false