scPDB - 3wid entry

Protein Data Bank Entry:

PDB ID : 3wid

Resolution :2.250 Å

Experimental Method : X-ray

Deposition Date : 2013-09-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glucose 1-dehydrogenase
ID:	Q979W2_THEVO
AC:	Q979W2
Organism:	Thermoplasma volcanium
Reign:	Archaea
TaxID:	273116
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	96 %
C	4 %

Ligand binding site composition:

B-Factor:	44.461
Number of residues:	50
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.878	1549.125

% Hydrophobic	% Polar
35.29	64.71
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	55.6 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
37.2411	-27.5807	35.7989

Binding mode :

What is Poseview ?

2D View
3D View

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
O3B	N	SER- 194	3.04	161.59	H-Bond (Protein Donor)	false
O2N	N	GLU- 197	3	151.42	H-Bond (Protein Donor)	false
C5D	CG	GLU- 197	4.11	0	Hydrophobic	false
O3B	ND2	ASN- 216	3.47	124.1	H-Bond (Protein Donor)	false
O2B	ND2	ASN- 216	3.2	169.87	H-Bond (Protein Donor)	false
O3X	NH1	ARG- 217	3.14	159.33	H-Bond (Protein Donor)	false
O3X	NH2	ARG- 217	3.39	144.38	H-Bond (Protein Donor)	false
O3X	CZ	ARG- 217	3.74	0	Ionic (Protein Cationic)	false
O2X	NE2	HIS- 218	2.59	170.02	H-Bond (Protein Donor)	false
N1A	OH	TYR- 238	2.61	165.95	H-Bond (Protein Donor)	false
C5D	CB	THR- 252	3.87	0	Hydrophobic	false
N6A	OG1	THR- 258	2.96	121.85	H-Bond (Ligand Donor)	false
N7N	O	PHE- 275	3.27	153.91	H-Bond (Ligand Donor)	false
C3N	CZ	PHE- 275	3.3	0	Hydrophobic	false
O3D	N	PHE- 277	3.31	141.52	H-Bond (Protein Donor)	false
O2D	O	PHE- 277	3.13	139.63	H-Bond (Ligand Donor)	false
N7N	O	SER- 304	3.1	149.13	H-Bond (Ligand Donor)	false
O7N	N	ASP- 306	3.09	169.97	H-Bond (Protein Donor)	false
O2N	O	HOH- 1127	2.83	150.7	H-Bond (Protein Donor)	false
O1N	O	HOH- 1167	2.79	179.96	H-Bond (Protein Donor)	false