scPDB - 4lfg entry

Protein Data Bank Entry:

PDB ID : 4lfg

Resolution :1.760 Å

Experimental Method : X-ray

Deposition Date : 2013-06-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative geranyltranstransferase
ID:	B9DUT7_STRU0
AC:	B9DUT7
Organism:	Streptococcus uberis
Reign:	Bacteria
TaxID:	218495
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	16.175
Number of residues:	28
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	2
Water Molecules:	4
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.046	735.750

% Hydrophobic	% Polar
38.07	61.93
According to VolSite

Ligand :

HET Code:	IPE
Formula:	C5H9O7P2
Molecular weight:	243.068 g/mol
DrugBank ID:	DB04714
Buried Surface Area:	59.66 %
Polar Surface area:	141.4 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	0
Rings:	0
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
36.2869	75.5598	4.07

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
O1A	NZ	LYS- 38	3.84	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 38	2.79	0	Ionic (Protein Cationic)	false
O3B	NZ	LYS- 38	2.73	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 38	2.79	135	H-Bond (Protein Donor)	false
O3B	NZ	LYS- 38	2.73	175.34	H-Bond (Protein Donor)	false
O3B	N	LYS- 38	2.82	167.73	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 41	3.78	0	Ionic (Protein Cationic)	false
O1A	NH1	ARG- 41	2.91	174.23	H-Bond (Protein Donor)	false
O2B	NE2	HIS- 71	2.76	160.83	H-Bond (Protein Donor)	false
C2	CD2	LEU- 75	3.62	0	Hydrophobic	false
O1B	NE	ARG- 90	2.94	177.8	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 90	2.72	165.4	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 90	3.75	0	Ionic (Protein Cationic)	false
O2B	CZ	ARG- 90	3.67	0	Ionic (Protein Cationic)	false
C5	CG2	THR- 173	3.83	0	Hydrophobic	false
C5	CE2	PHE- 209	4.43	0	Hydrophobic	false
O2B	O	HOH- 416	2.74	179.95	H-Bond (Protein Donor)	false