scPDB - 3tut entry

Protein Data Bank Entry:

PDB ID : 3tut

Resolution :1.580 Å

Experimental Method : X-ray

Deposition Date : 2011-09-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	RNA 3'-terminal phosphate cyclase
ID:	RTCA_ECOLI
AC:	P46849
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	6.5.1.4

Chains:

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

Ligand binding site composition:

B-Factor:	22.632
Number of residues:	37
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.592	995.625

% Hydrophobic	% Polar
36.61	63.39
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	67.96 %
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
14.3873	-9.45358	-15.2311

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
O2G	N	GLY- 17	2.79	164.32	H-Bond (Protein Donor)	false
O1B	N	GLN- 18	2.99	157.81	H-Bond (Protein Donor)	false
O3G	CZ	ARG- 21	3.74	0	Ionic (Protein Cationic)	false
O3G	NH1	ARG- 21	2.8	163.93	H-Bond (Protein Donor)	false
O3B	NH2	ARG- 21	3.45	171.5	H-Bond (Protein Donor)	false
O2G	NE	ARG- 40	3.16	155.67	H-Bond (Protein Donor)	false
O2B	CZ	ARG- 43	3.45	0	Ionic (Protein Cationic)	false
O2B	NH1	ARG- 43	2.94	151.92	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 43	3.09	143.1	H-Bond (Protein Donor)	false
O3G	NE2	GLN- 51	3.22	160.26	H-Bond (Protein Donor)	false
O3G	NE2	HIS- 52	2.66	156.97	H-Bond (Protein Donor)	false
C4'	CD2	LEU- 101	3.77	0	Hydrophobic	false
O2A	OG	SER- 129	2.62	155.42	H-Bond (Protein Donor)	false
C1'	CG	PRO- 131	4.39	0	Hydrophobic	false
C2'	CD1	TYR- 284	4.21	0	Hydrophobic	false
O3'	OD1	ASP- 287	2.78	152.01	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 287	2.64	163.31	H-Bond (Ligand Donor)	false
O2'	NE2	GLN- 288	3.05	146.3	H-Bond (Protein Donor)	false
N3	NE2	GLN- 288	3.2	137.28	H-Bond (Protein Donor)	false
O1A	ND2	ASN- 309	2.81	143.18	H-Bond (Protein Donor)	false
N6	O	HOH- 384	2.75	142.63	H-Bond (Ligand Donor)	false