scPDB - 3tzl entry

Protein Data Bank Entry:

PDB ID : 3tzl

Resolution :2.150 Å

Experimental Method : X-ray

Deposition Date : 2011-09-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Tryptophan--tRNA ligase
ID:	SYW_CAMJE
AC:	Q9PIB4
Organism:	Campylobacter jejuni subsp. jejuni serotype O:2
Reign:	Bacteria
TaxID:	192222
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	49.906
Number of residues:	32
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	NA

Cavity properties

Ligandability	Volume (Å3)
0.949	813.375

% Hydrophobic	% Polar
45.64	54.36
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	51.54 %
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
48.9333	18.1212	32.1055

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
O1B	NE2	HIS- 14	3.31	146.82	H-Bond (Protein Donor)	false
O2B	NE2	HIS- 14	3.24	156.59	H-Bond (Protein Donor)	false
O3A	ND2	ASN- 17	3.29	157.64	H-Bond (Protein Donor)	false
C1'	CB	ALA- 21	4.29	0	Hydrophobic	false
N6	O	VAL- 182	2.93	160.82	H-Bond (Ligand Donor)	false
N1	N	VAL- 182	3.01	157.35	H-Bond (Protein Donor)	false
N6	O	MET- 190	2.76	168.04	H-Bond (Ligand Donor)	false
O2B	NZ	LYS- 192	3.1	171.6	H-Bond (Protein Donor)	false
O2B	N	LYS- 192	2.91	172.45	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 192	3.1	0	Ionic (Protein Cationic)	false