scPDB - 4d2d entry

Protein Data Bank Entry:

PDB ID : 4d2d

Resolution :2.520 Å

Experimental Method : X-ray

Deposition Date : 2014-05-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Di-or tripeptide:H+ symporter
ID:	Q5M4H8_STRT2
AC:	Q5M4H8
Organism:	Streptococcus thermophilus
Reign:	Bacteria
TaxID:	264199
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	42.117
Number of residues:	26
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.000	1157.625

% Hydrophobic	% Polar
44.02	55.98
According to VolSite

Ligand :

HET Code:	ALA_ALA_ALA
Formula:	C9H17N3O4
Molecular weight:	231.249 g/mol
DrugBank ID:	-
Buried Surface Area:	54.49 %
Polar Surface area:	125.97 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	0
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
-22.9191	-18.8484	-0.930313

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
CB	CZ	TYR- 30	3.57	0	Hydrophobic	false
CB	CE1	TYR- 30	4.45	0	Hydrophobic	false
N	OH	TYR- 30	3.4	138.46	H-Bond (Ligand Donor)	false
CB	CE1	TYR- 68	4.4	0	Hydrophobic	false
CB	CZ3	TRP- 296	3.92	0	Hydrophobic	false
O	OE1	GLU- 299	2.6	130.7	H-Bond (Protein Donor)	false
CB	CB	SER- 303	4.23	0	Hydrophobic	false
OXT	OG	SER- 303	3.47	125.42	H-Bond (Protein Donor)	false
OXT	N	SER- 303	3.36	122.06	H-Bond (Protein Donor)	false