scPDB - 1xli entry

Protein Data Bank Entry:

PDB ID : 1xli

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 1991-10-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Xylose isomerase
ID:	XYLA_ARTS7
AC:	P12070
Organism:	Arthrobacter sp.
Reign:	Bacteria
TaxID:	1669
EC Number:	5.3.1.5

Chains:

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

Ligand binding site composition:

B-Factor:	12.640
Number of residues:	26
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:
Metals:	MN MN

Cavity properties

Ligandability	Volume (Å3)
0.166	435.375

% Hydrophobic	% Polar
37.21	62.79
According to VolSite

Ligand :

HET Code:	GLT
Formula:	C6H12O5S
Molecular weight:	196.221 g/mol
DrugBank ID:	-
Buried Surface Area:	66.55 %
Polar Surface area:	126.45 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	5
Rings:	1
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	1

Mass center Coordinates

X	Y	Z
26.1046	75.6184	10.511

Binding mode :

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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
C5	CZ2	TRP- 15	4.21	0	Hydrophobic	false
O1	NE2	HIS- 53	3.05	123.46	H-Bond (Protein Donor)	false
C6	CG2	THR- 89	3.97	0	Hydrophobic	false
O6	OG1	THR- 89	2.85	161.31	H-Bond (Protein Donor)	false
C1	CZ	PHE- 93	3.66	0	Hydrophobic	false
S5	CE1	PHE- 93	3.79	0	Hydrophobic	false
C6	CG1	VAL- 134	3.92	0	Hydrophobic	false
C3	CD2	TRP- 136	4.43	0	Hydrophobic	false
C6	CB	TRP- 136	4.32	0	Hydrophobic	false
C1	CE3	TRP- 136	3.52	0	Hydrophobic	false
O4	OE1	GLU- 180	2.73	146.66	H-Bond (Ligand Donor)	false
O3	MN	MN- 399	2.48	0	Metal Acceptor	false
O4	MN	MN- 399	1.9	0	Metal Acceptor	false
O2	O	HOH- 911	2.67	158.01	H-Bond (Protein Donor)	false
O4	O	HOH- 912	3.06	137.58	H-Bond (Protein Donor)	false