scPDB - 3zy3 entry

Protein Data Bank Entry:

PDB ID : 3zy3

Resolution :1.860 Å

Experimental Method : X-ray

Deposition Date : 2011-08-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	GDP-fucose protein O-fucosyltransferase 1
ID:	OFUT1_CAEEL
AC:	Q18014
Organism:	Caenorhabditis elegans
Reign:	Eukaryota
TaxID:	6239
EC Number:	2.4.1.221

Chains:

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

Ligand binding site composition:

B-Factor:	24.964
Number of residues:	38
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.364	580.500

% Hydrophobic	% Polar
48.84	51.16
According to VolSite

Ligand :

HET Code:	GDP
Formula:	C10H12N5O11P2
Molecular weight:	440.177 g/mol
DrugBank ID:	DB04315
Buried Surface Area:	71.4 %
Polar Surface area:	276.39 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-9.27071	59.3968	-22.6117

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
C4'	CB	ARG- 40	3.92	0	Hydrophobic	false
O3'	N	PHE- 41	3.18	129.37	H-Bond (Protein Donor)	false
O2A	N	GLY- 42	2.69	148.72	H-Bond (Protein Donor)	false
O1A	N	ASN- 43	3.11	149.09	H-Bond (Protein Donor)	false
N7	NE2	HIS- 238	3.03	158.71	H-Bond (Protein Donor)	false
O1B	NH2	ARG- 240	2.89	171	H-Bond (Protein Donor)	false
O2B	NE	ARG- 240	2.72	153.11	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 240	3.71	0	Ionic (Protein Cationic)	false
O2B	CZ	ARG- 240	3.6	0	Ionic (Protein Cationic)	false
C1'	CB	ASP- 309	4.1	0	Hydrophobic	false
N1	OD1	ASP- 334	2.91	144.56	H-Bond (Ligand Donor)	false
N2	OD1	ASP- 334	2.81	146.69	H-Bond (Ligand Donor)	false
C2'	CE	MET- 336	3.68	0	Hydrophobic	false
O2B	OG	SER- 355	2.64	165.55	H-Bond (Protein Donor)	false
O3B	OG1	THR- 356	2.93	168.28	H-Bond (Protein Donor)	false
O3B	N	THR- 356	2.74	161.95	H-Bond (Protein Donor)	false
O3A	OG1	THR- 356	3.31	124.47	H-Bond (Protein Donor)	false
C3'	CD1	PHE- 357	3.72	0	Hydrophobic	false
C2'	CE1	PHE- 357	4.18	0	Hydrophobic	false
O4'	O	HOH- 2009	3.01	179.96	H-Bond (Protein Donor)	false