scPDB - 1xid entry

Protein Data Bank Entry:

PDB ID : 1xid

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 1994-03-07

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_STRRU
AC:	P24300
Organism:	Streptomyces rubiginosus
Reign:	Bacteria
TaxID:	1929
EC Number:	5.3.1.5

Chains:

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

Ligand binding site composition:

B-Factor:	5.025
Number of residues:	25
Including
Standard Amino Acids:	23
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	MN MN

Cavity properties

Ligandability	Volume (Å3)
0.373	766.125

% Hydrophobic	% Polar
33.48	66.52
According to VolSite

Ligand :

HET Code:	ASC
Formula:	C6H7O6
Molecular weight:	175.116 g/mol
DrugBank ID:	DB00126
Buried Surface Area:	65.17 %
Polar Surface area:	110.05 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	3
Rings:	1
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
35.4914	32.1093	57.5571

Binding mode :

What is Poseview ?

2D View
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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
O1	NE2	HIS- 54	2.78	147.35	H-Bond (Protein Donor)	false
O4	NE2	HIS- 54	3.48	142.61	H-Bond (Protein Donor)	false
C6	CZ	PHE- 94	4.05	0	Hydrophobic	false
C4	CE3	TRP- 137	3.47	0	Hydrophobic	false
C5	CZ3	TRP- 137	4.49	0	Hydrophobic	false
O5	OD2	ASP- 287	2.94	125.48	H-Bond (Ligand Donor)	false
O6	NZ	LYS- 289	2.77	165.3	H-Bond (Protein Donor)	false
O2	MN	MN- 391	2.36	0	Metal Acceptor	false
O3	MN	MN- 391	2.49	0	Metal Acceptor	false