scPDB - 3a5y entry

Protein Data Bank Entry:

PDB ID : 3a5y

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2009-08-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Elongation factor P--(R)-beta-lysine ligase
ID:	EPMA_ECOLI
AC:	P0A8N7
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	20.572
Number of residues:	47
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.795	1248.750

% Hydrophobic	% Polar
31.35	68.65
According to VolSite

Ligand :

HET Code:	KAA
Formula:	C16H27N8O7S
Molecular weight:	475.500 g/mol
DrugBank ID:	-
Buried Surface Area:	72.05 %
Polar Surface area:	257.5 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
0.0208125	26.8415	31.5464

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
NZ	OE2	GLU- 78	3.17	122.04	H-Bond (Ligand Donor)	false
NZ	OE1	GLU- 78	3.43	131.59	H-Bond (Ligand Donor)	false
NZ	OE2	GLU- 78	3.17	0	Ionic (Ligand Cationic)	false
NZ	OE1	GLU- 78	3.43	0	Ionic (Ligand Cationic)	false
N	OE1	GLU- 78	3.49	0	Ionic (Ligand Cationic)	false
O	NH2	ARG- 100	2.79	157.87	H-Bond (Protein Donor)	false
O1S	NH1	ARG- 100	2.89	173.88	H-Bond (Protein Donor)	false
N6	OE1	GLU- 102	2.9	147.3	H-Bond (Ligand Donor)	false
N1	N	ASN- 109	3.27	161.02	H-Bond (Protein Donor)	false
N6	O	ASN- 109	3.12	126.65	H-Bond (Ligand Donor)	false
C1'	CE2	PHE- 112	3.71	0	Hydrophobic	false
DuAr	DuAr	PHE- 112	3.51	0	Aromatic Face/Face	false
C5'	CE	MET- 114	3.7	0	Hydrophobic	false
C4'	SD	MET- 114	3.76	0	Hydrophobic	false
C1'	SD	MET- 114	4.4	0	Hydrophobic	false
NZ	OH	TYR- 118	2.97	168.69	H-Bond (Ligand Donor)	false
O3'	OE2	GLU- 244	2.77	158.22	H-Bond (Ligand Donor)	false
O2'	O	GLU- 244	3.18	175.25	H-Bond (Ligand Donor)	false
CG	CZ	PHE- 249	3.48	0	Hydrophobic	false
NZ	OE2	GLU- 251	2.71	154.51	H-Bond (Ligand Donor)	false
NZ	OE1	GLU- 251	3.46	148.31	H-Bond (Ligand Donor)	false
NZ	OE2	GLU- 251	2.71	0	Ionic (Ligand Cationic)	false
NZ	OE1	GLU- 251	3.46	0	Ionic (Ligand Cationic)	false
C5'	CB	ALA- 298	3.89	0	Hydrophobic	false
CB	CB	ALA- 298	3.66	0	Hydrophobic	false
O2'	N	GLY- 300	3.19	120.08	H-Bond (Protein Donor)	false
C2'	CD	ARG- 303	4.12	0	Hydrophobic	false
O2S	O	HOH- 693	2.66	123.85	H-Bond (Protein Donor)	false
N7	O	HOH- 742	3.01	179.96	H-Bond (Protein Donor)	false
N3	O	HOH- 758	2.93	165.22	H-Bond (Protein Donor)	false