scPDB - 2tys entry

Protein Data Bank Entry:

PDB ID : 2tys

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 1997-01-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Tryptophan synthase beta chain
ID:	TRPB_SALTY
AC:	P0A2K1
Organism:	Salmonella typhimurium
Reign:	Bacteria
TaxID:	99287
EC Number:	4.2.1.20

Chains:

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

Ligand binding site composition:

B-Factor:	17.196
Number of residues:	51
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.106	334.125

% Hydrophobic	% Polar
55.56	44.44
According to VolSite

Ligand :

HET Code:	PLT
Formula:	C19H17N3O7P
Molecular weight:	430.328 g/mol
DrugBank ID:	-
Buried Surface Area:	88.93 %
Polar Surface area:	183.63 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	2
Rings:	3
Aromatic rings:	3
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
80.8668	15.2016	11.9967

Binding mode :

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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
C2A	CB	ALA- 85	3.71	0	Hydrophobic	false
NE1	OE2	GLU- 109	2.55	160.17	H-Bond (Ligand Donor)	false
CZ2	CG	GLU- 109	3.93	0	Hydrophobic	false
O	OG1	THR- 110	2.53	133.2	H-Bond (Protein Donor)	false
OXT	N	GLY- 111	2.62	148.01	H-Bond (Protein Donor)	false
C3	CB	ALA- 112	4.44	0	Hydrophobic	false
OXT	N	ALA- 112	2.8	163.41	H-Bond (Protein Donor)	false
C2A	CG	GLN- 114	4.42	0	Hydrophobic	false
O	N	HIS- 115	2.8	158.4	H-Bond (Protein Donor)	false
CB	CD1	LEU- 166	4.18	0	Hydrophobic	false
CE2	CD2	LEU- 166	3.65	0	Hydrophobic	false
CE3	CD1	LEU- 166	3.53	0	Hydrophobic	false
CZ2	SG	CYS- 170	3.64	0	Hydrophobic	false
CZ2	CD1	LEU- 188	4.43	0	Hydrophobic	false
O1P	OG1	THR- 190	2.81	167.21	H-Bond (Protein Donor)	false
CH2	CG2	THR- 190	3.31	0	Hydrophobic	false
O2P	N	GLY- 232	2.67	151.77	H-Bond (Protein Donor)	false
O2P	N	GLY- 233	2.78	157.21	H-Bond (Protein Donor)	false
O2P	N	GLY- 234	2.83	166.36	H-Bond (Protein Donor)	false
O1P	N	SER- 235	3.03	150.85	H-Bond (Protein Donor)	false
O1P	OG	SER- 235	2.62	175.35	H-Bond (Protein Donor)	false
O3P	N	ASN- 236	2.68	166.26	H-Bond (Protein Donor)	false
O3P	ND2	ASN- 236	2.78	149.79	H-Bond (Protein Donor)	false
C5A	CD2	LEU- 304	3.81	0	Hydrophobic	false
CZ3	CB	PHE- 306	4.03	0	Hydrophobic	false
C2A	CB	ALA- 348	3.89	0	Hydrophobic	false
C4	CG	GLU- 350	3.93	0	Hydrophobic	false
N1	OG	SER- 377	2.6	168.11	H-Bond (Protein Donor)	false
C2A	CB	SER- 377	4.34	0	Hydrophobic	false