scPDB - 1s4o entry

Protein Data Bank Entry:

PDB ID : 1s4o

Resolution :2.010 Å

Experimental Method : X-ray

Deposition Date : 2004-01-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glycolipid 2-alpha-mannosyltransferase
ID:	KRE2_YEAST
AC:	P27809
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	4 %
B	96 %

Ligand binding site composition:

B-Factor:	22.213
Number of residues:	31
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
0.382	2068.875

% Hydrophobic	% Polar
37.03	62.97
According to VolSite

Ligand :

HET Code:	GDP
Formula:	C10H12N5O11P2
Molecular weight:	440.177 g/mol
DrugBank ID:	DB04315
Buried Surface Area:	63.31 %
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
46.3868	55.8425	47.0806

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
O3'	O	LEU- 128	2.58	153.33	H-Bond (Ligand Donor)	false
C1'	CD1	LEU- 128	3.76	0	Hydrophobic	false
N7	NE	ARG- 130	3.42	132.04	H-Bond (Protein Donor)	false
O2'	OE1	GLU- 133	3.47	127.2	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 133	2.66	155.09	H-Bond (Ligand Donor)	false
N2	OD1	ASN- 160	2.84	133.92	H-Bond (Ligand Donor)	false
N1	OD1	ASP- 161	2.72	146.39	H-Bond (Ligand Donor)	false
N2	OD1	ASP- 161	3.04	132.34	H-Bond (Ligand Donor)	false
O3B	OH	TYR- 214	2.69	146.39	H-Bond (Protein Donor)	false
O1B	OH	TYR- 220	2.52	165.6	H-Bond (Protein Donor)	false
C5'	CE	MET- 223	3.99	0	Hydrophobic	false
C1'	CG	MET- 223	4.28	0	Hydrophobic	false
C3'	CG	GLU- 247	3.6	0	Hydrophobic	false
C3'	CG	PRO- 248	4.49	0	Hydrophobic	false
O2B	MN	MN- 602	2.31	0	Metal Acceptor	false
O1A	MN	MN- 602	2.23	0	Metal Acceptor	false
O3'	O	HOH- 968	2.89	161.77	H-Bond (Protein Donor)	false
O2B	O	HOH- 976	2.61	160.07	H-Bond (Protein Donor)	false
N1	O	HOH- 1066	3.43	127.82	H-Bond (Ligand Donor)	false