scPDB - 3tdv entry

Protein Data Bank Entry:

PDB ID : 3tdv

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2011-08-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Gentamicin resistance protein
ID:	P96762_ENTGA
AC:	P96762
Organism:	Enterococcus gallinarum
Reign:	Bacteria
TaxID:	1353
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	24.030
Number of residues:	35
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.873	1464.750

% Hydrophobic	% Polar
38.48	61.52
According to VolSite

Ligand :

HET Code:	GDP
Formula:	C10H12N5O11P2
Molecular weight:	440.177 g/mol
DrugBank ID:	DB04315
Buried Surface Area:	71.95 %
Polar Surface area:	276.39 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
29.9492	-12.4405	-42.659

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
C1'	CG	LEU- 27	4.17	0	Hydrophobic	false
O1B	N	ARG- 32	2.69	146.2	H-Bond (Protein Donor)	false
O1B	N	ASN- 33	2.79	131.52	H-Bond (Protein Donor)	false
O3B	ND2	ASN- 33	2.84	164.95	H-Bond (Protein Donor)	false
O1A	NH2	ARG- 45	2.92	141.81	H-Bond (Protein Donor)	false
O1A	NE	ARG- 45	2.86	145.76	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 45	3.3	0	Ionic (Protein Cationic)	false
N7	OH	TYR- 92	2.68	143.17	H-Bond (Protein Donor)	false
O6	N	VAL- 95	2.94	142.02	H-Bond (Protein Donor)	false
N1	O	VAL- 95	3.35	163.51	H-Bond (Ligand Donor)	false
C2'	CD1	ILE- 99	4.21	0	Hydrophobic	false
C2'	CD1	ILE- 217	3.81	0	Hydrophobic	false
O2B	MG	MG- 501	2.11	0	Metal Acceptor	false
O2A	MG	MG- 501	2.09	0	Metal Acceptor	false
O3B	MG	MG- 502	2.1	0	Metal Acceptor	false
N2	O	HOH- 513	2.79	174.05	H-Bond (Ligand Donor)	false