scPDB - 3d2e entry

Protein Data Bank Entry:

PDB ID : 3d2e

Resolution :2.350 Å

Experimental Method : X-ray

Deposition Date : 2008-05-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Heat shock protein homolog SSE1
ID:	HSP7F_YEAST
AC:	P32589
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	92 %
B	8 %

Ligand binding site composition:

B-Factor:	33.797
Number of residues:	49
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.561	972.000

% Hydrophobic	% Polar
27.43	72.57
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	75.2 %
Polar Surface area:	319.88 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
86.5515	81.7598	178.559

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
O1G	N	ASN- 11	2.71	152.7	H-Bond (Protein Donor)	false
O1B	N	ASN- 12	2.87	154.85	H-Bond (Protein Donor)	false
O1B	N	ASN- 13	3.05	166.86	H-Bond (Protein Donor)	false
O1A	ND2	ASN- 13	3.38	133.9	H-Bond (Protein Donor)	false
N6	O	GLN- 33	3.19	152.3	H-Bond (Ligand Donor)	false
N6	OE1	GLN- 33	3.19	160.62	H-Bond (Ligand Donor)	false
O1G	NZ	LYS- 69	2.86	157.2	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 69	2.86	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 69	3.81	0	Ionic (Protein Cationic)	false
O3B	N	HIS- 206	3.04	160.82	H-Bond (Protein Donor)	false
O3A	N	HIS- 206	3.13	130.51	H-Bond (Protein Donor)	false
C4'	CB	HIS- 206	4.34	0	Hydrophobic	false
O3'	ND1	HIS- 206	3.22	131.3	H-Bond (Ligand Donor)	false
O2G	OG	SER- 207	2.56	162.12	H-Bond (Protein Donor)	false
O2G	N	SER- 207	2.89	136.72	H-Bond (Protein Donor)	false
O2G	N	SER- 208	3.22	133.56	H-Bond (Protein Donor)	false
O2'	OE2	GLU- 272	2.77	175.63	H-Bond (Ligand Donor)	false
O2'	NZ	LYS- 275	2.62	160.28	H-Bond (Protein Donor)	false
N1	OG	SER- 279	2.68	169.76	H-Bond (Protein Donor)	false
O2A	N	GLY- 343	2.95	163.64	H-Bond (Protein Donor)	false
O5'	N	GLY- 343	3.36	133.3	H-Bond (Protein Donor)	false
O4'	OG1	THR- 344	3.41	153.9	H-Bond (Protein Donor)	false
N7	NH1	ARG- 346	2.99	148.22	H-Bond (Protein Donor)	false
O3G	MG	MG- 2001	2.19	0	Metal Acceptor	false
O2B	MG	MG- 2001	2.11	0	Metal Acceptor	false
N3	O	HOH- 2060	2.96	179.96	H-Bond (Protein Donor)	false