scPDB - 4f79 entry

Protein Data Bank Entry:

PDB ID : 4f79

Resolution :2.540 Å

Experimental Method : X-ray

Deposition Date : 2012-05-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative phospho-beta-glucosidase
ID:	Q8DT00_STRMU
AC:	Q8DT00
Organism:	Streptococcus mutans serotype c
Reign:	Bacteria
TaxID:	210007
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	58.020
Number of residues:	32
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.674	816.750

% Hydrophobic	% Polar
46.28	53.72
According to VolSite

Ligand :

HET Code:	P53
Formula:	C13H17O10P
Molecular weight:	364.242 g/mol
DrugBank ID:	-
Buried Surface Area:	72.35 %
Polar Surface area:	181.61 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	2
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
34.4883	2.40917	9.48942

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
O34	OE1	GLN- 18	2.74	154.53	H-Bond (Ligand Donor)	false
O36	NE2	GLN- 18	2.62	159.7	H-Bond (Protein Donor)	false
O32	NE2	HIS- 130	3.36	131.25	H-Bond (Protein Donor)	false
O34	NE2	HIS- 130	2.93	156.54	H-Bond (Protein Donor)	false
C21	CE2	PHE- 131	3.81	0	Hydrophobic	false
O32	ND2	ASN- 175	3.02	127.84	H-Bond (Protein Donor)	false
O32	OE1	GLU- 176	2.9	127.99	H-Bond (Ligand Donor)	false
C13	CD2	TYR- 313	3.8	0	Hydrophobic	false
C19	CE2	TYR- 313	3.92	0	Hydrophobic	false
C27	CZ	TYR- 313	3.92	0	Hydrophobic	false
C13	CE	MET- 314	4.2	0	Hydrophobic	false
C13	CH2	TRP- 349	4.36	0	Hydrophobic	false
C38	CH2	TRP- 349	4.03	0	Hydrophobic	false
C1	CH2	TRP- 349	3.38	0	Hydrophobic	false
C23	CZ2	TRP- 423	3.65	0	Hydrophobic	false
C27	CE2	TRP- 423	3.64	0	Hydrophobic	false
O2P	N	ALA- 431	2.68	163.65	H-Bond (Protein Donor)	false
C6	CB	ALA- 431	4.08	0	Hydrophobic	false
C25	CB	ALA- 431	3.54	0	Hydrophobic	false
O3P	N	GLY- 432	2.84	155.31	H-Bond (Protein Donor)	false
O1P	NZ	LYS- 438	2.85	139.89	H-Bond (Protein Donor)	false
O1P	NZ	LYS- 438	2.85	0	Ionic (Protein Cationic)	false
O3P	NZ	LYS- 438	3.71	0	Ionic (Protein Cationic)	false
O1P	OH	TYR- 440	2.65	137.1	H-Bond (Protein Donor)	false
C38	CZ	TYR- 440	4.16	0	Hydrophobic	false