scPDB - 3nd6 entry

Protein Data Bank Entry:

PDB ID : 3nd6

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2010-06-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Phosphopantetheine adenylyltransferase
ID:	COAD_ENTFA
AC:	Q831P9
Organism:	Enterococcus faecalis
Reign:	Bacteria
TaxID:	226185
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	34.186
Number of residues:	38
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.513	513.000

% Hydrophobic	% Polar
30.92	69.08
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	58.41 %
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
-8.53419	-29.5459	17.2797

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
C4'	CE1	PHE- 7	3.72	0	Hydrophobic	false
O2A	N	SER- 10	3.38	146.87	H-Bond (Protein Donor)	false
O2A	NE2	HIS- 18	3.47	130.79	H-Bond (Protein Donor)	false
O3A	NE2	HIS- 18	2.92	156.81	H-Bond (Protein Donor)	false
C1'	CD1	LEU- 21	4.17	0	Hydrophobic	false
O3'	N	GLY- 90	3.24	161.04	H-Bond (Protein Donor)	false
O3'	O	GLY- 90	3.43	135.17	H-Bond (Ligand Donor)	false
O2'	O	GLY- 90	2.86	145.82	H-Bond (Ligand Donor)	false
N6	O	TYR- 125	2.98	122.47	H-Bond (Ligand Donor)	false
N6	O	VAL- 128	3.05	135.68	H-Bond (Ligand Donor)	false
O2B	N	SER- 130	2.74	169.24	H-Bond (Protein Donor)	false
O1G	N	SER- 131	2.9	154.71	H-Bond (Protein Donor)	false
O1G	OG	SER- 131	3.36	139.87	H-Bond (Protein Donor)	false
O1B	O	HOH- 233	2.98	180	H-Bond (Protein Donor)	false
O3B	O	HOH- 286	3.13	144.86	H-Bond (Protein Donor)	false