scPDB - 2ivp entry

Protein Data Bank Entry:

PDB ID : 2ivp

Resolution :2.500 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:	29.191
Number of residues:	42
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	FE2

Cavity properties

Ligandability	Volume (Å3)
1.321	1005.750

% Hydrophobic	% Polar
52.35	47.65
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	67.32 %
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
-27.9848	9.78781	-10.5376

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
O2B	N	GLY- 130	2.67	139.1	H-Bond (Protein Donor)	false
O3G	N	GLY- 131	3.09	143.76	H-Bond (Protein Donor)	false
O3'	OD1	ASP- 159	3.39	120.43	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 159	2.53	158.72	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 159	2.67	129.63	H-Bond (Ligand Donor)	false
C3'	CZ	PHE- 169	4.23	0	Hydrophobic	false
C2'	CB	PRO- 170	4.35	0	Hydrophobic	false
O2'	N	GLY- 172	3.09	138.57	H-Bond (Protein Donor)	false
N6	OE1	GLU- 176	2.92	151.81	H-Bond (Ligand Donor)	false
O2A	N	GLY- 253	3.29	125.23	H-Bond (Protein Donor)	false
C1'	CG2	VAL- 254	3.9	0	Hydrophobic	false
N1	ND2	ASN- 257	3.02	160.03	H-Bond (Protein Donor)	false
O2A	N	ASP- 285	3.32	151.04	H-Bond (Protein Donor)	false
O1G	FE	FE2- 1326	2.47	0	Metal Acceptor	false