scPDB - 2a8s entry

Protein Data Bank Entry:

PDB ID : 2a8s

Resolution :2.450 Å

Experimental Method : X-ray

Deposition Date : 2005-07-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	U8 snoRNA-decapping enzyme
ID:	NUD16_XENLA
AC:	Q6TEC1
Organism:	Xenopus laevis
Reign:	Eukaryota
TaxID:	8355
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	98 %
B	2 %

Ligand binding site composition:

B-Factor:	52.110
Number of residues:	41
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	5
Water Molecules:	1
Cofactors:
Metals:	MN MN MN MN

Cavity properties

Ligandability	Volume (Å3)
0.696	536.625

% Hydrophobic	% Polar
61.64	38.36
According to VolSite

Ligand :

HET Code:	GTP
Formula:	C10H12N5O14P3
Molecular weight:	519.149 g/mol
DrugBank ID:	DB04137
Buried Surface Area:	64.85 %
Polar Surface area:	335.56 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
23.3188	52.2794	2.85044

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	NE2	HIS- 37	3.33	166.95	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 63	3.62	0	Ionic (Protein Cationic)	false
O2A	NH2	ARG- 63	3.16	150.73	H-Bond (Protein Donor)	false
O2A	NH1	ARG- 63	3.18	149.24	H-Bond (Protein Donor)	false
O6	N	PHE- 70	3.18	168.64	H-Bond (Protein Donor)	false
O1B	N	PHE- 74	2.86	127.67	H-Bond (Protein Donor)	false
C5'	CE2	PHE- 74	3.23	0	Hydrophobic	false
C4'	CZ	PHE- 74	3.72	0	Hydrophobic	false
N2	OG1	THR- 122	3.47	125.21	H-Bond (Ligand Donor)	false
C2'	CG1	ILE- 178	3.98	0	Hydrophobic	false
N1	OE1	GLN- 184	2.62	150.29	H-Bond (Ligand Donor)	false
N2	OE1	GLN- 184	3.27	125.99	H-Bond (Ligand Donor)	false
O2B	MN	MN- 300	2	0	Metal Acceptor	false
O1A	MN	MN- 300	2.08	0	Metal Acceptor	false
O3G	MN	MN- 301	2.49	0	Metal Acceptor	false
O2B	MN	MN- 301	2.53	0	Metal Acceptor	false
O1G	MN	MN- 302	1.86	0	Metal Acceptor	false
O2G	MN	MN- 302	2.78	0	Metal Acceptor	false
O3G	MN	MN- 302	2.11	0	Metal Acceptor	false
O2G	MN	MN- 303	2.41	0	Metal Acceptor	false
O3G	MN	MN- 303	2.47	0	Metal Acceptor	false
O3B	MN	MN- 303	2.43	0	Metal Acceptor	false