scPDB - 1up6 entry

Protein Data Bank Entry:

PDB ID : 1up6

Resolution :2.550 Å

Experimental Method : X-ray

Deposition Date : 2003-09-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	6-phospho-beta-glucosidase BglT
ID:	BGLT_THEMA
AC:	Q9X108
Organism:	Thermotoga maritima
Reign:	Bacteria
TaxID:	243274
EC Number:	3.2.1.86

Chains:

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

Ligand binding site composition:

B-Factor:	21.582
Number of residues:	47
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
0.738	1036.125

% Hydrophobic	% Polar
43.97	56.03
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	73.34 %
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
152.261	65.6209	94.0275

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
O2N	OG	SER- 10	2.73	155.28	H-Bond (Protein Donor)	false
C5B	CB	SER- 10	3.55	0	Hydrophobic	false
O3B	OD2	ASP- 36	3.23	138.81	H-Bond (Ligand Donor)	false
O2B	OD2	ASP- 36	3.43	138.51	H-Bond (Ligand Donor)	false
C1B	CG1	ILE- 37	4.47	0	Hydrophobic	false
O2A	NZ	LYS- 41	3.32	124.94	H-Bond (Protein Donor)	false
O3B	NZ	LYS- 41	2.7	163.71	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 41	3.32	0	Ionic (Protein Cationic)	false
C1B	CB	PHE- 79	4.15	0	Hydrophobic	false
O3D	O	PHE- 79	3.22	156.37	H-Bond (Ligand Donor)	false
O1A	CZ	ARG- 80	3.97	0	Ionic (Protein Cationic)	false
O1N	CZ	ARG- 80	3.96	0	Ionic (Protein Cationic)	false
O1A	NE	ARG- 80	2.85	146.73	H-Bond (Protein Donor)	false
C5B	CB	ARG- 80	4.38	0	Hydrophobic	false
C3D	CB	ARG- 80	3.64	0	Hydrophobic	false
O2D	OE2	GLU- 103	2.76	121.62	H-Bond (Ligand Donor)	false
N1A	OH	TYR- 123	2.69	168.92	H-Bond (Protein Donor)	false
C3N	CB	PHE- 138	4.14	0	Hydrophobic	false
N7N	O	PHE- 138	3.27	165.09	H-Bond (Ligand Donor)	false
O3D	N	ASN- 140	3.07	172.5	H-Bond (Protein Donor)	false
O2D	ND2	ASN- 140	3.45	147.29	H-Bond (Protein Donor)	false
N7N	O	LEU- 161	3.14	125.43	H-Bond (Ligand Donor)	false
O7N	N	ASN- 163	2.84	134.95	H-Bond (Protein Donor)	false
C4N	CB	TYR- 294	4.11	0	Hydrophobic	false
O7N	MN	MN- 1417	2.25	0	Metal Acceptor	false