scPDB - 3vet entry

Protein Data Bank Entry:

PDB ID : 3vet

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2012-01-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	nebramycin 5' synthase
ID:	TOBZ_STRSD
AC:	Q70IY1
Organism:	Streptoalloteichus tenebrarius
Reign:	Bacteria
TaxID:	1933
EC Number:	6.1.2.2

Chains:

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

Ligand binding site composition:

B-Factor:	25.541
Number of residues:	45
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	FE2

Cavity properties

Ligandability	Volume (Å3)
1.013	1360.125

% Hydrophobic	% Polar
40.45	59.55
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	76.68 %
Polar Surface area:	260.7 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
16.7816	30.8579	9.5907

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
O2B	NE2	HIS- 14	2.79	159.47	H-Bond (Protein Donor)	false
O1B	N	GLY- 138	2.68	122.51	H-Bond (Protein Donor)	false
O1B	N	GLN- 139	2.83	153.24	H-Bond (Protein Donor)	false
O2'	O	GLY- 168	2.88	150.31	H-Bond (Ligand Donor)	false
O3'	OE2	GLU- 172	2.77	167.18	H-Bond (Ligand Donor)	false
C2'	CG	GLU- 172	4.22	0	Hydrophobic	false
C2'	CG	PRO- 185	4.24	0	Hydrophobic	false
O1A	N	GLY- 310	3.21	143.75	H-Bond (Protein Donor)	false
C1'	CG2	VAL- 311	4.14	0	Hydrophobic	false
N1	ND2	ASN- 314	2.71	166.91	H-Bond (Protein Donor)	false
O2A	N	ASP- 338	2.95	152.56	H-Bond (Protein Donor)	false
O3B	FE	FE2- 607	2.23	0	Metal Acceptor	false
O1A	FE	FE2- 607	2.1	0	Metal Acceptor	false