scPDB - 1ga8 entry

Protein Data Bank Entry:

PDB ID : 1ga8

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2000-11-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	LgtC
ID:	Q93EK7_NEIME
AC:	Q93EK7
Organism:	Neisseria meningitidis
Reign:	Bacteria
TaxID:	487
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	11.026
Number of residues:	48
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	2
Water Molecules:	3
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
0.306	357.750

% Hydrophobic	% Polar
53.77	46.23
According to VolSite

Ligand :

HET Code:	UPF
Formula:	C15H21FN2O16P2
Molecular weight:	566.277 g/mol
DrugBank ID:	DB02976
Buried Surface Area:	84.43 %
Polar Surface area:	296.59 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	6
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
26.8188	47.1004	61.7474

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
O2'	O	ALA- 6	2.51	134.3	H-Bond (Ligand Donor)	false
N3	OD1	ASP- 8	2.69	156.18	H-Bond (Ligand Donor)	false
O2	N	ASP- 8	3.1	136.57	H-Bond (Protein Donor)	false
O4	ND2	ASN- 10	3.11	164.51	H-Bond (Protein Donor)	false
C2D	CD2	TYR- 11	4.04	0	Hydrophobic	false
C3D	CE2	TYR- 11	4.31	0	Hydrophobic	false
C6'	CD1	ILE- 76	4.43	0	Hydrophobic	false
C5D	CG2	ILE- 79	3.75	0	Hydrophobic	false
C5'	CD1	ILE- 79	3.6	0	Hydrophobic	false
C1D	CB	THR- 83	4.49	0	Hydrophobic	false
C5D	CB	THR- 83	3.6	0	Hydrophobic	false
O6'	OG1	THR- 83	3.28	175.18	H-Bond (Protein Donor)	false
O3'	NH1	ARG- 86	3.03	142.16	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 103	3.03	149.84	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 103	2.6	141.65	H-Bond (Ligand Donor)	false
O3D	N	ILE- 104	2.87	168.38	H-Bond (Protein Donor)	false
C2D	CG1	ILE- 104	3.67	0	Hydrophobic	false
C6'	CB	GLN- 187	4.21	0	Hydrophobic	false
O6'	NE2	GLN- 187	3.05	142.69	H-Bond (Protein Donor)	false
O4'	OD1	ASP- 188	3.09	153.37	H-Bond (Ligand Donor)	false
F2'	CB	CYS- 246	4.11	0	Hydrophobic	false
O2B	N	GLY- 247	2.7	169.43	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 250	2.85	149.3	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 250	2.85	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 250	3.55	0	Ionic (Protein Cationic)	false
O1A	MN	MN- 400	2.25	0	Metal Acceptor	false
O1B	MN	MN- 400	2.23	0	Metal Acceptor	false