scPDB - 1yro entry

Protein Data Bank Entry:

PDB ID : 1yro

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2005-02-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Beta-1,4-galactosyltransferase 1
ID:	B4GT1_BOVIN
AC:	P08037
Organism:	Bos taurus
Reign:	Eukaryota
TaxID:	9913
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	26.234
Number of residues:	43
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
0.511	1819.125

% Hydrophobic	% Polar
38.40	61.60
According to VolSite

Ligand :

HET Code:	GDU
Formula:	C15H22N2O17P2
Molecular weight:	564.286 g/mol
DrugBank ID:	DB03501
Buried Surface Area:	73.32 %
Polar Surface area:	316.82 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	7
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
29.1763	32.9528	23.9691

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
O2D	O	PRO- 187	2.66	154.89	H-Bond (Ligand Donor)	false
C4D	CG	PRO- 187	4.35	0	Hydrophobic	false
C1D	CG	PRO- 187	4.08	0	Hydrophobic	false
N3	O	ARG- 189	2.79	174.94	H-Bond (Ligand Donor)	false
O2	N	ARG- 189	3.04	133.78	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 191	3.93	0	Ionic (Protein Cationic)	false
O1A	NH2	ARG- 191	3.06	158.24	H-Bond (Protein Donor)	false
C1D	CZ	PHE- 226	3.53	0	Hydrophobic	false
O3'	NZ	LYS- 228	2.68	151.37	H-Bond (Protein Donor)	false
C4D	CD	LYS- 228	4.2	0	Hydrophobic	false
C4'	CD	LYS- 228	3.91	0	Hydrophobic	false
O3'	OD1	ASP- 252	2.74	164.39	H-Bond (Ligand Donor)	false
C3D	CB	ASP- 252	4.21	0	Hydrophobic	false
O2D	N	VAL- 253	2.91	159.82	H-Bond (Protein Donor)	false
C2D	CG1	VAL- 253	3.56	0	Hydrophobic	false
O3D	OD2	ASP- 254	3.28	125.74	H-Bond (Ligand Donor)	false
O3'	N	GLY- 292	3.18	149.61	H-Bond (Protein Donor)	false
O1B	NE1	TRP- 314	2.71	152	H-Bond (Protein Donor)	false
C6'	CE2	TRP- 314	3.45	0	Hydrophobic	false
O6'	N	GLY- 315	2.77	154.69	H-Bond (Protein Donor)	false
O4'	OE1	GLU- 317	2.71	148.24	H-Bond (Ligand Donor)	false
O6'	OE1	GLU- 317	2.93	147.39	H-Bond (Ligand Donor)	false
O6'	OE2	GLU- 317	2.79	140.86	H-Bond (Ligand Donor)	false
O1A	MN	MN- 529	2.2	0	Metal Acceptor	false
O2B	MN	MN- 529	2.11	0	Metal Acceptor	false
O4	O	HOH- 924	2.77	148.73	H-Bond (Protein Donor)	false
O2A	O	HOH- 946	2.6	179.96	H-Bond (Protein Donor)	false