scPDB - 1x1j entry

Protein Data Bank Entry:

PDB ID : 1x1j

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2005-04-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Xanthan lyase
ID:	XANLY_BACGL
AC:	Q9AQS0
Organism:	Bacillus sp.
Reign:	Bacteria
TaxID:	84635
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	23.016
Number of residues:	30
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.788	1505.250

% Hydrophobic	% Polar
34.53	65.47
According to VolSite

Ligand :

HET Code:	46D
Formula:	C15H20O14
Molecular weight:	424.311 g/mol
DrugBank ID:	DB04596
Buried Surface Area:	55.11 %
Polar Surface area:	227.55 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	5
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
15.4078	57.913	80.2346

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
O2	ND2	ASN- 146	3.49	125.89	H-Bond (Protein Donor)	false
O3	ND2	ASN- 146	2.98	162.73	H-Bond (Protein Donor)	false
O2	OD1	ASN- 146	3.23	151.02	H-Bond (Ligand Donor)	false
C5	CZ2	TRP- 147	4.07	0	Hydrophobic	false
C1	CZ2	TRP- 147	3.6	0	Hydrophobic	false
C2	CE2	TRP- 147	4.1	0	Hydrophobic	false
CP1	CE2	TRP- 148	4.1	0	Hydrophobic	false
CP4	CH2	TRP- 148	4.25	0	Hydrophobic	false
CP3	CZ2	TRP- 148	4.14	0	Hydrophobic	false
C4	CB	TRP- 148	4.25	0	Hydrophobic	false
CP5	CE3	TRP- 148	3.48	0	Hydrophobic	false
CP8	CZ3	TRP- 148	3.74	0	Hydrophobic	false
CP3	CH2	TRP- 197	3.78	0	Hydrophobic	false
O6A	NE2	HIS- 246	2.94	168.76	H-Bond (Protein Donor)	false
OP1	OH	TYR- 255	2.57	137.11	H-Bond (Protein Donor)	false
C5	CZ	TYR- 255	4.11	0	Hydrophobic	false
CP2	CE1	TYR- 255	3.59	0	Hydrophobic	false
OP1	NH2	ARG- 309	3.14	156.42	H-Bond (Protein Donor)	false
OP7	CZ	ARG- 313	3.36	0	Ionic (Protein Cationic)	false
OP3	NH1	ARG- 313	3.1	168.96	H-Bond (Protein Donor)	false
OP2	NH2	ARG- 313	2.76	155.6	H-Bond (Protein Donor)	false
OP7	OH	TYR- 315	2.77	153.98	H-Bond (Protein Donor)	false
O2	ND2	ASN- 424	3.18	163.97	H-Bond (Protein Donor)	false
OP8	CZ	ARG- 612	3.77	0	Ionic (Protein Cationic)	false
OP8	NH1	ARG- 612	2.79	151.06	H-Bond (Protein Donor)	false
O6A	O	HOH- 3087	3.2	179.96	H-Bond (Protein Donor)	false