scPDB - 2ivn entry

Protein Data Bank Entry:

PDB ID : 2ivn

Resolution :1.650 Å

Experimental Method : X-ray

Deposition Date : 2006-06-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	tRNA N6-adenosine threonylcarbamoyltransferase
ID:	KAE1_PYRAB
AC:	Q9UXT7
Organism:	Pyrococcus abyssi
Reign:	Archaea
TaxID:	272844
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	17.831
Number of residues:	46
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
1.251	887.625

% Hydrophobic	% Polar
53.23	46.77
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	69.75 %
Polar Surface area:	322.68 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
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
3.05287	60.03	10.8385

Binding mode :

What is Poseview ?

2D View
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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
O1G	NE2	HIS- 107	2.98	159.36	H-Bond (Protein Donor)	false
O3G	OG	SER- 129	2.63	164.58	H-Bond (Protein Donor)	false
O2B	N	GLY- 130	2.67	143.69	H-Bond (Protein Donor)	false
O3G	N	GLY- 131	3.4	158.26	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 159	2.67	165.72	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 159	2.71	135.95	H-Bond (Ligand Donor)	false
C3'	CE1	PHE- 169	4.44	0	Hydrophobic	false
C2'	CB	PRO- 170	4.12	0	Hydrophobic	false
O2'	N	GLY- 172	3.08	148.41	H-Bond (Protein Donor)	false
N6	OE1	GLU- 176	2.8	149.08	H-Bond (Ligand Donor)	false
C1'	CG2	VAL- 254	3.87	0	Hydrophobic	false
N1	ND2	ASN- 257	2.98	159.47	H-Bond (Protein Donor)	false
O2G	OD2	ASP- 285	2.66	177.43	H-Bond (Protein Donor)	false
O2A	N	ASP- 285	3.06	160.49	H-Bond (Protein Donor)	false
N3B	OD1	ASP- 285	2.91	130.46	H-Bond (Ligand Donor)	false
N3B	OD2	ASP- 285	2.91	145.52	H-Bond (Ligand Donor)	false
O2A	MG	MG- 1328	2.21	0	Metal Acceptor	false
O1B	O	HOH- 2175	2.88	136.39	H-Bond (Protein Donor)	false