scPDB - 4rp8 entry

Protein Data Bank Entry:

PDB ID : 4rp8

Resolution :2.360 Å

Experimental Method : X-ray

Deposition Date : 2014-10-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ascorbate-specific PTS system EIIC component
ID:	ULAA_ECOLI
AC:	P39301
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	34.370
Number of residues:	21
Including
Standard Amino Acids:	21
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.611	330.750

% Hydrophobic	% Polar
43.88	56.12
According to VolSite

Ligand :

HET Code:	ASC
Formula:	C6H7O6
Molecular weight:	175.116 g/mol
DrugBank ID:	DB00126
Buried Surface Area:	73.98 %
Polar Surface area:	110.05 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	3
Rings:	1
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
-22.6663	2.19067	-7.21275

Binding mode :

What is Poseview ?

2D View
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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
O2	OG1	THR- 86	3.01	142.85	H-Bond (Protein Donor)	false
O5	NE2	HIS- 135	2.95	154.78	H-Bond (Protein Donor)	false
O2	NE2	GLN- 139	2.71	148.14	H-Bond (Protein Donor)	false
O5	NE2	HIS- 194	2.89	171.51	H-Bond (Protein Donor)	false
O1	NE2	GLN- 195	3.07	168.79	H-Bond (Protein Donor)	false
O5	OD2	ASP- 314	2.67	149.27	H-Bond (Ligand Donor)	false
O6	OD2	ASP- 314	3.21	159.91	H-Bond (Ligand Donor)	false
O6	OD1	ASP- 314	2.65	132.63	H-Bond (Ligand Donor)	false
C4	CG2	ILE- 358	4.28	0	Hydrophobic	false
C4	CD2	PHE- 362	4.16	0	Hydrophobic	false
C6	CD1	PHE- 362	3.49	0	Hydrophobic	false