scPDB - 3a8t entry

Protein Data Bank Entry:

PDB ID : 3a8t

Resolution :2.370 Å

Experimental Method : X-ray

Deposition Date : 2009-10-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Adenylate isopentenyltransferase
ID:	IPT_HUMLU
AC:	Q5GHF7
Organism:	Humulus lupulus
Reign:	Eukaryota
TaxID:	3486
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	26.211
Number of residues:	28
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.234	496.125

% Hydrophobic	% Polar
47.62	52.38
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	61.71 %
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
28.0239	28.1323	23.2921

Binding mode :

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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
N6	OD2	ASP- 62	3.29	179.05	H-Bond (Ligand Donor)	false
O1G	NZ	LYS- 63	3.77	0	Ionic (Protein Cationic)	false
O2G	NZ	LYS- 63	3.14	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 63	3.28	0	Ionic (Protein Cationic)	false
O2G	NZ	LYS- 63	3.14	143.94	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 63	3.28	140.05	H-Bond (Protein Donor)	false
C3'	CE	MET- 64	4.35	0	Hydrophobic	false
C2'	CG	MET- 64	3.93	0	Hydrophobic	false
N6	O	THR- 74	2.64	166.71	H-Bond (Ligand Donor)	false
O2A	OG	SER- 129	2.85	148.81	H-Bond (Protein Donor)	false
O3A	OG	SER- 129	3.23	125.42	H-Bond (Protein Donor)	false
O1B	N	SER- 131	3.22	149.52	H-Bond (Protein Donor)	false
O2B	OG	SER- 131	2.71	160.4	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 220	3.97	0	Ionic (Protein Cationic)	false
C2'	CB	LYS- 220	4.43	0	Hydrophobic	false
C1'	CG1	ILE- 222	4.11	0	Hydrophobic	false
N3	N	ILE- 222	2.87	169.73	H-Bond (Protein Donor)	false
C1'	CD2	LEU- 268	3.69	0	Hydrophobic	false
C5'	CD1	LEU- 268	4.06	0	Hydrophobic	false
O3G	NZ	LYS- 275	3.53	0	Ionic (Protein Cationic)	false
O1B	NZ	LYS- 275	3.96	0	Ionic (Protein Cationic)	false