scPDB - 5dw0 entry

Protein Data Bank Entry:

PDB ID : 5dw0

Resolution :2.010 Å

Experimental Method : X-ray

Deposition Date : 2015-09-22

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 1
ID:	TRPB1_PYRFU
AC:	Q8U093
Organism:	Pyrococcus furiosus
Reign:	Archaea
TaxID:	186497
EC Number:	4.2.1.20

Chains:

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

Ligand binding site composition:

B-Factor:	34.664
Number of residues:	40
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.764	354.375

% Hydrophobic	% Polar
59.05	40.95
According to VolSite

Ligand :

HET Code:	PLS
Formula:	C11H15N2O8P
Molecular weight:	334.219 g/mol
DrugBank ID:	-
Buried Surface Area:	83.25 %
Polar Surface area:	192.32 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	3
Rings:	1
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-2.94155	-39.0545	-45.3894

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
C2A	CB	ALA- 80	3.94	0	Hydrophobic	false
O3P	NZ	LYS- 82	3.19	142.14	H-Bond (Protein Donor)	false
O3P	NZ	LYS- 82	3.19	0	Ionic (Protein Cationic)	false
O	OG1	THR- 105	2.59	162.39	H-Bond (Protein Donor)	false
O	N	GLY- 106	2.91	164.47	H-Bond (Protein Donor)	false
CA	CB	ALA- 107	4.48	0	Hydrophobic	false
OG	N	ALA- 107	2.9	154.71	H-Bond (Protein Donor)	false
C2A	CG	GLN- 109	4.42	0	Hydrophobic	false
C3	CB	GLN- 109	4.48	0	Hydrophobic	false
OXT	N	HIS- 110	2.92	159.4	H-Bond (Protein Donor)	false
CB	CD2	LEU- 161	4.28	0	Hydrophobic	false
O3P	OG	SER- 185	2.76	173.82	H-Bond (Protein Donor)	false
O1P	N	GLY- 227	2.76	141.86	H-Bond (Protein Donor)	false
O1P	N	GLY- 229	2.77	136.37	H-Bond (Protein Donor)	false
O3P	N	GLY- 229	3.41	143.85	H-Bond (Protein Donor)	false
O3P	N	SER- 230	3.01	149.97	H-Bond (Protein Donor)	false
O2P	ND2	ASN- 231	2.93	152.52	H-Bond (Protein Donor)	false
O2P	N	ASN- 231	2.95	165.3	H-Bond (Protein Donor)	false
C5A	CD2	LEU- 299	3.93	0	Hydrophobic	false
OG	OD1	ASP- 300	2.8	144.08	H-Bond (Ligand Donor)	false
C2A	CB	ALA- 343	4.23	0	Hydrophobic	false
C2A	CG	GLU- 345	4.46	0	Hydrophobic	false
C5	CG	GLU- 345	3.91	0	Hydrophobic	false
N1	OG	SER- 371	2.86	160.95	H-Bond (Protein Donor)	false
O1P	O	HOH- 527	2.83	179.98	H-Bond (Protein Donor)	false