scPDB - 3zec entry

Protein Data Bank Entry:

PDB ID : 3zec

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2012-12-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Adenosine monophosphate-protein transferase SoFic
ID:	SOFIC_SHEON
AC:	Q8E9K5
Organism:	Shewanella oneidensis
Reign:	Bacteria
TaxID:	211586
EC Number:	2.7.7.n1

Chains:

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

Ligand binding site composition:

B-Factor:	18.940
Number of residues:	38
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.982	789.750

% Hydrophobic	% Polar
53.85	46.15
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	67.02 %
Polar Surface area:	322.68 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
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
18.2921	22.0675	-3.66816

Binding mode :

What is Poseview ?

2D View
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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
C2'	CG	GLU- 195	4.5	0	Hydrophobic	false
C1'	CB	GLU- 195	4.16	0	Hydrophobic	false
O2B	N	GLY- 203	2.95	130.05	H-Bond (Protein Donor)	false
O2A	N	ASN- 204	3.15	151.78	H-Bond (Protein Donor)	false
O2A	ND2	ASN- 204	2.89	161.19	H-Bond (Protein Donor)	false
O3A	N	GLY- 205	2.88	163.44	H-Bond (Protein Donor)	false
O1B	NE	ARG- 206	2.92	168.43	H-Bond (Protein Donor)	false
O1B	N	ARG- 206	2.89	165.53	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 206	2.77	162.17	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 206	3.84	0	Ionic (Protein Cationic)	false
O2B	CZ	ARG- 206	3.66	0	Ionic (Protein Cationic)	false
O1G	CZ	ARG- 209	3.64	0	Ionic (Protein Cationic)	false
O1G	NH2	ARG- 209	2.91	166.77	H-Bond (Protein Donor)	false
O1G	NH1	ARG- 209	3.47	134.67	H-Bond (Protein Donor)	false
O2G	NH2	ARG- 209	3.02	120.99	H-Bond (Protein Donor)	false
O3'	NH1	ARG- 209	2.93	161.41	H-Bond (Protein Donor)	false
O2'	OH	TYR- 240	2.98	145.93	H-Bond (Ligand Donor)	false
C2'	CE2	TYR- 240	3.86	0	Hydrophobic	false
C3'	CZ	TYR- 241	4.06	0	Hydrophobic	false
C2'	CE1	TYR- 241	4.4	0	Hydrophobic	false
C2'	CD1	LEU- 244	3.91	0	Hydrophobic	false