scPDB - 1vjt entry

Protein Data Bank Entry:

PDB ID : 1vjt

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2004-03-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Alpha-glucosidase, putative
ID:	Q9WZL1_THEMA
AC:	Q9WZL1
Organism:	Thermotoga maritima
Reign:	Bacteria
TaxID:	243274
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	29.627
Number of residues:	36
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.050	1117.125

% Hydrophobic	% Polar
40.79	59.21
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	65.03 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
65.9311	6.13506	12.3971

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
C5B	CB	SER- 10	4.3	0	Hydrophobic	false
O3B	OD2	ASP- 38	2.89	175.57	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 38	2.85	169.49	H-Bond (Ligand Donor)	false
O2B	OD2	ASP- 38	3.44	137.03	H-Bond (Ligand Donor)	false
O2B	ND1	HIS- 40	2.65	163.02	H-Bond (Protein Donor)	false
C3B	CD	ARG- 43	4.48	0	Hydrophobic	false
C5B	CB	TYR- 85	3.55	0	Hydrophobic	false
C5D	CB	TYR- 85	4.06	0	Hydrophobic	false
C3D	CD2	TYR- 85	3.67	0	Hydrophobic	false
O4B	N	TYR- 85	3.34	163.4	H-Bond (Protein Donor)	false
C2B	CE2	TYR- 87	4.21	0	Hydrophobic	false
C4D	CB	ALA- 159	4.37	0	Hydrophobic	false
O3D	N	ASN- 160	3.39	159.53	H-Bond (Protein Donor)	false
O1A	NE	ARG- 310	2.93	140.64	H-Bond (Protein Donor)	false
O1A	NH2	ARG- 310	3	134.84	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 310	3.37	0	Ionic (Protein Cationic)	false
O2A	CZ	ARG- 310	3.77	0	Ionic (Protein Cationic)	false