scPDB - 1tae entry

Protein Data Bank Entry:

PDB ID : 1tae

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2004-05-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	DNA ligase
ID:	DNLJ_ENTFA
AC:	Q837V6
Organism:	Enterococcus faecalis
Reign:	Bacteria
TaxID:	226185
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	29.077
Number of residues:	46
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.664	1721.250

% Hydrophobic	% Polar
41.76	58.24
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	71.71 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
-7.91377	60.264	31.8909

Binding mode :

What is Poseview ?

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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
C4N	CB	TYR- 25	4.33	0	Hydrophobic	false
DuAr	DuAr	TYR- 29	3.7	0	Aromatic Face/Face	false
C4N	CB	TYR- 29	3.4	0	Hydrophobic	false
N7N	O	VAL- 37	2.76	167.07	H-Bond (Ligand Donor)	false
N7N	OD2	ASP- 39	2.91	151.78	H-Bond (Ligand Donor)	false
C2D	CD1	TYR- 42	4.22	0	Hydrophobic	false
C3N	CB	TYR- 42	3.79	0	Hydrophobic	false
DuAr	DuAr	TYR- 42	3.79	0	Aromatic Face/Face	false
O2D	OD2	ASP- 43	3.15	127.62	H-Bond (Ligand Donor)	false
O2D	OD1	ASP- 43	2.72	167.34	H-Bond (Ligand Donor)	false
O3	OG	SER- 88	3.16	121.39	H-Bond (Protein Donor)	false
O1N	OG	SER- 88	2.73	152.96	H-Bond (Protein Donor)	false
C5B	CD1	LEU- 89	3.48	0	Hydrophobic	false
O2A	OD2	ASP- 91	2.54	169.62	H-Bond (Protein Donor)	false
N6A	OE2	GLU- 118	2.94	151.79	H-Bond (Ligand Donor)	false
O1A	NZ	LYS- 120	3.17	146.97	H-Bond (Protein Donor)	false
O4B	NZ	LYS- 120	3.02	138.33	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 120	3.17	0	Ionic (Protein Cationic)	false
C1B	CG	LYS- 120	4.46	0	Hydrophobic	false
N7A	N	ILE- 121	3.02	131.09	H-Bond (Protein Donor)	false
O1N	NH1	ARG- 141	3.09	134.95	H-Bond (Protein Donor)	false
O1N	NH2	ARG- 141	2.71	157.29	H-Bond (Protein Donor)	false
O1N	CZ	ARG- 141	3.32	0	Ionic (Protein Cationic)	false
O2B	OE2	GLU- 175	2.71	169.89	H-Bond (Ligand Donor)	false
C2B	CZ	TYR- 227	4.42	0	Hydrophobic	false
DuAr	DuAr	TYR- 227	3.62	0	Aromatic Face/Face	false
N1A	NZ	LYS- 291	2.81	148.34	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 315	3.13	125.89	H-Bond (Protein Donor)	false
O3D	NZ	LYS- 315	2.86	122.37	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 315	3.13	0	Ionic (Protein Cationic)	false