scPDB - 2yy5 entry

Protein Data Bank Entry:

PDB ID : 2yy5

Resolution :2.550 Å

Experimental Method : X-ray

Deposition Date : 2007-04-27

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_MYCPN
AC:	P75510
Organism:	Mycoplasma pneumoniae
Reign:	Bacteria
TaxID:	272634
EC Number:	6.1.1.2

Chains:

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

Ligand binding site composition:

B-Factor:	21.238
Number of residues:	47
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.956	1326.375

% Hydrophobic	% Polar
33.33	66.67
According to VolSite

Ligand :

HET Code:	WSA
Formula:	C21H24N8O7S
Molecular weight:	532.530 g/mol
DrugBank ID:	-
Buried Surface Area:	77.06 %
Polar Surface area:	245.65 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	5
Rings:	5
Aromatic rings:	4
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
51.4231	9.74319	108.5

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
CZ3	CB	THR- 7	4.28	0	Hydrophobic	false
C5'	CG2	ILE- 9	4.08	0	Hydrophobic	false
O	NE2	GLN- 10	2.79	138.9	H-Bond (Protein Donor)	false
O1S	N	GLN- 10	2.93	155.89	H-Bond (Protein Donor)	false
O4'	ND2	ASN- 19	2.98	164.54	H-Bond (Protein Donor)	false
C4'	CG2	VAL- 23	3.98	0	Hydrophobic	false
CB	CB	ALA- 41	4.39	0	Hydrophobic	false
CE2	CG	MET- 137	3.37	0	Hydrophobic	false
CZ3	CE	MET- 137	3.86	0	Hydrophobic	false
CZ2	CB	ASP- 140	4.35	0	Hydrophobic	false
N11	OD2	ASP- 140	3.29	158.6	H-Bond (Ligand Donor)	false
CZ2	CG1	ILE- 141	4.05	0	Hydrophobic	false
CH2	CG1	VAL- 149	3.71	0	Hydrophobic	false
CZ3	CG1	VAL- 151	3.54	0	Hydrophobic	false
O3'	N	GLY- 152	3.09	149.65	H-Bond (Protein Donor)	false
O2'	N	GLY- 152	3.03	126.14	H-Bond (Protein Donor)	false
O2'	OD1	ASP- 154	2.7	159.37	H-Bond (Ligand Donor)	false
C2'	CG	GLN- 155	4.18	0	Hydrophobic	false
N1	N	ILE- 191	2.74	150.76	H-Bond (Protein Donor)	false
N6	O	ILE- 191	2.87	162	H-Bond (Ligand Donor)	false
N6	O	MET- 201	3.16	159.92	H-Bond (Ligand Donor)	false
O3'	O	HOH- 1400	2.81	142.53	H-Bond (Ligand Donor)	false