scPDB - 1v1b entry

Protein Data Bank Entry:

PDB ID : 1v1b

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2004-04-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	2-dehydro-3-deoxygluconokinase
ID:	KDGK_THET8
AC:	Q53W83
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	300852
EC Number:	2.7.1.45

Chains:

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

Ligand binding site composition:

B-Factor:	48.590
Number of residues:	42
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.872	357.750

% Hydrophobic	% Polar
50.94	49.06
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	61.41 %
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
9.50694	33.6536	102.203

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
C3'	CB	LYS- 219	4.22	0	Hydrophobic	false
O3'	O	GLY- 224	3.23	171.01	H-Bond (Ligand Donor)	false
O3G	N	GLY- 250	2.74	139.82	H-Bond (Protein Donor)	false
O1B	N	GLY- 250	2.78	127.09	H-Bond (Protein Donor)	false
O2G	OD2	ASP- 251	2.88	148.47	H-Bond (Protein Donor)	false
C4'	CB	PHE- 253	4.08	0	Hydrophobic	false
C3'	CD1	PHE- 253	4.22	0	Hydrophobic	false