scPDB - 3lki entry

Protein Data Bank Entry:

PDB ID : 3lki

Resolution :2.040 Å

Experimental Method : X-ray

Deposition Date : 2010-01-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Fructokinase
ID:	Q87CC0_XYLFT
AC:	Q87CC0
Organism:	Xylella fastidiosa
Reign:	Bacteria
TaxID:	183190
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	37.475
Number of residues:	41
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.228	583.875

% Hydrophobic	% Polar
41.62	58.38
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	58.95 %
Polar Surface area:	319.88 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
24.3921	5.70342	19.0092

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
O1G	NH2	ARG- 178	3.05	124.67	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 203	2.8	134.84	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 203	2.8	0	Ionic (Protein Cationic)	false
O2A	OG1	THR- 238	3.27	137.57	H-Bond (Protein Donor)	false
C3'	CG1	VAL- 244	4.22	0	Hydrophobic	false
C2'	CG2	THR- 257	3.73	0	Hydrophobic	false
C5'	CB	ALA- 268	4.09	0	Hydrophobic	false
O2G	N	GLY- 269	3.26	131.22	H-Bond (Protein Donor)	false
O3B	N	GLY- 269	3.28	126.58	H-Bond (Protein Donor)	false
C5'	CB	PHE- 272	4	0	Hydrophobic	false
C4'	CD1	PHE- 272	3.82	0	Hydrophobic	false