scPDB - 1y8q entry

Protein Data Bank Entry:

PDB ID : 1y8q

Resolution :2.250 Å

Experimental Method : X-ray

Deposition Date : 2004-12-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	SUMO-activating enzyme subunit 2
ID:	SAE2_HUMAN
AC:	Q9UBT2
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	6.3.2

Chains:

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

Ligand binding site composition:

B-Factor:	30.584
Number of residues:	41
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.742	1201.500

% Hydrophobic	% Polar
34.55	65.45
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	61.9 %
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
21.7108	-8.314	6.19

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
O1A	N	GLY- 27	2.98	162.55	H-Bond (Protein Donor)	false
O3'	OD1	ASP- 48	2.74	148.66	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 48	3.47	152.71	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 48	2.6	154.03	H-Bond (Ligand Donor)	false
N3	N	LEU- 49	3.42	146.24	H-Bond (Protein Donor)	false
C2'	CD1	LEU- 49	4.22	0	Hydrophobic	false
C2'	CB	ASP- 50	4.5	0	Hydrophobic	false
O1B	NE2	GLN- 60	3.47	164.58	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 72	2.79	123.32	H-Bond (Protein Donor)	false
O3'	NZ	LYS- 72	2.91	168.34	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 72	2.79	0	Ionic (Protein Cationic)	false
N6	OG	SER- 95	3.23	130.87	H-Bond (Ligand Donor)	false
N1	N	ILE- 96	3.2	154.57	H-Bond (Protein Donor)	false
C1'	CD2	LEU- 116	4.16	0	Hydrophobic	false
C5'	CB	ASP- 117	3.97	0	Hydrophobic	false
O2G	NZ	LYS- 346	2.98	153.35	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 346	2.98	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 346	3.75	0	Ionic (Protein Cationic)	false
O2G	MG	MG- 641	2	0	Metal Acceptor	false
O2B	MG	MG- 641	2.11	0	Metal Acceptor	false