scPDB - 4rdi entry

Protein Data Bank Entry:

PDB ID : 4rdi

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2014-09-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	tRNA threonylcarbamoyladenosine dehydratase
ID:	TCDA_ECOLI
AC:	Q46927
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	6.1

Chains:

Chain Name:	Percentage of Residues within binding site
C	3 %
D	97 %

Ligand binding site composition:

B-Factor:	25.859
Number of residues:	32
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.447	756.000

% Hydrophobic	% Polar
41.96	58.04
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	61.31 %
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
50.9187	54.2824	42.641

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
O1A	N	GLY- 40	2.86	155.66	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 61	2.54	161.89	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 61	2.63	154.52	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 61	3.29	127.05	H-Bond (Ligand Donor)	false
O2G	NH2	ARG- 72	2.97	146.84	H-Bond (Protein Donor)	false
O2G	CZ	ARG- 72	3.95	0	Ionic (Protein Cationic)	false
O2B	NE2	GLN- 73	2.76	155	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 85	3.95	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 85	2.64	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 85	2.64	136.02	H-Bond (Protein Donor)	false
O3'	NZ	LYS- 85	2.68	164.4	H-Bond (Protein Donor)	false
N6	O	VAL- 109	2.94	156.34	H-Bond (Ligand Donor)	false
N1	N	VAL- 109	2.96	158.64	H-Bond (Protein Donor)	false
C5'	CB	ASP- 130	4.38	0	Hydrophobic	false
N7	OG	SER- 131	2.93	136.62	H-Bond (Protein Donor)	false
O5'	O	HOH- 479	3.4	179.96	H-Bond (Protein Donor)	false