scPDB - 3e78 entry

Protein Data Bank Entry:

PDB ID : 3e78

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2008-08-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	High affinity transport system protein p37
ID:	P37_MYCHR
AC:	P15363
Organism:	Mycoplasma hyorhinis
Reign:	Bacteria
TaxID:	2100
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	23.573
Number of residues:	35
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.302	644.625

% Hydrophobic	% Polar
40.84	59.16
According to VolSite

Ligand :

HET Code:	TPP
Formula:	C12H16N4O7P2S
Molecular weight:	422.291 g/mol
DrugBank ID:	-
Buried Surface Area:	62.83 %
Polar Surface area:	225.32 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
33.026	31.4512	31.9222

Binding mode :

What is Poseview ?

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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
C7	CB	ALA- 126	4.09	0	Hydrophobic	false
O3A	NZ	LYS- 129	3.49	128.16	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 129	2.93	156.55	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 129	2.93	0	Ionic (Protein Cationic)	false
O3B	NZ	LYS- 129	3.52	0	Ionic (Protein Cationic)	false
CM2	CG1	VAL- 201	3.31	0	Hydrophobic	false
CM4	CD2	TYR- 215	3.68	0	Hydrophobic	false
C7	CZ	TYR- 215	3.6	0	Hydrophobic	false
O1B	OH	TYR- 215	2.68	173.71	H-Bond (Protein Donor)	false
O3B	OG	SER- 255	2.59	160.75	H-Bond (Protein Donor)	false
O2B	N	SER- 256	2.94	166.2	H-Bond (Protein Donor)	false
O1B	OG	SER- 257	2.56	153.87	H-Bond (Protein Donor)	false
O1B	N	SER- 257	2.89	150.54	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 258	2.79	0	Ionic (Protein Cationic)	false
O3B	NZ	LYS- 258	2.92	0	Ionic (Protein Cationic)	false
O3B	NZ	LYS- 258	2.92	150.02	H-Bond (Protein Donor)	false
CM4	CG	GLU- 308	3.76	0	Hydrophobic	false
CM2	CB	TRP- 314	4.16	0	Hydrophobic	false
CM4	CH2	TRP- 314	4.27	0	Hydrophobic	false
CM4	CE2	TYR- 343	4.5	0	Hydrophobic	false
C6	CE2	TYR- 343	3.88	0	Hydrophobic	false