scPDB - 2ixb entry

Protein Data Bank Entry:

PDB ID : 2ixb

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2006-07-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Alpha-N-acetylgalactosaminidase
ID:	GH109_ELIME
AC:	A4Q8F7
Organism:	Elizabethkingia meningoseptica
Reign:	Bacteria
TaxID:	238
EC Number:	3.2.1.49

Chains:

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

Ligand binding site composition:

B-Factor:	40.508
Number of residues:	54
Including
Standard Amino Acids:	50
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.905	941.625

% Hydrophobic	% Polar
41.58	58.42
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	74.31 %
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
-14.75	41.6207	-0.1865

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
C4B	CB	ALA- 27	4.03	0	Hydrophobic	false
C1B	CB	ALA- 27	3.96	0	Hydrophobic	false
O2A	N	LEU- 30	3.07	176.91	H-Bond (Protein Donor)	false
O2N	N	ARG- 31	2.79	161.02	H-Bond (Protein Donor)	false
C5D	CB	ARG- 31	4.35	0	Hydrophobic	false
C5N	CB	ARG- 31	3.83	0	Hydrophobic	false
C4N	CD	ARG- 31	3.6	0	Hydrophobic	false
O3B	OD1	ASP- 52	3.16	158.63	H-Bond (Ligand Donor)	false
O3B	OD2	ASP- 52	2.74	134.61	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 52	2.59	147.53	H-Bond (Ligand Donor)	false
C3B	CG	MET- 57	4.43	0	Hydrophobic	false
N6A	O	ASN- 80	3.12	139.48	H-Bond (Ligand Donor)	false
C5B	CG	PRO- 100	4.43	0	Hydrophobic	false
O2D	NE1	TRP- 101	3.07	168.93	H-Bond (Protein Donor)	false
C4D	CB	GLU- 121	4.33	0	Hydrophobic	false
N7N	OE2	GLU- 121	3.31	134.99	H-Bond (Ligand Donor)	false
O3D	O	VAL- 122	3.15	150.04	H-Bond (Ligand Donor)	false
O7N	ND2	ASN- 150	2.81	138.1	H-Bond (Protein Donor)	false
N7N	OD1	ASN- 150	3.07	162.55	H-Bond (Ligand Donor)	false
O2A	OG	SER- 208	2.76	156.73	H-Bond (Protein Donor)	false
O1N	OE1	GLU- 209	2.63	163.65	H-Bond (Protein Donor)	false
O1A	NE1	TRP- 212	2.92	161.59	H-Bond (Protein Donor)	false
C5D	CZ2	TRP- 212	4.01	0	Hydrophobic	false
C3D	CH2	TRP- 212	3.68	0	Hydrophobic	false
O2D	OH	TYR- 225	2.73	144.2	H-Bond (Ligand Donor)	false
O2N	O	HOH- 2020	2.87	171.99	H-Bond (Protein Donor)	false