scPDB - 1on3 entry

Protein Data Bank Entry:

PDB ID : 1on3

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2003-02-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Methylmalonyl-CoA carboxyltransferase 12S subunit
ID:	12S_PROFR
AC:	Q8GBW6
Organism:	Propionibacterium freudenreichii subsp. shermanii
Reign:	Bacteria
TaxID:	1752
EC Number:	2.1.3.1

Chains:

Chain Name:	Percentage of Residues within binding site
B	71 %
E	29 %

Ligand binding site composition:

B-Factor:	23.237
Number of residues:	42
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.703	425.250

% Hydrophobic	% Polar
44.44	55.56
According to VolSite

Ligand :

HET Code:	MCA
Formula:	C25H35N7O19P3S
Molecular weight:	862.567 g/mol
DrugBank ID:	DB04045
Buried Surface Area:	41.21 %
Polar Surface area:	469.81 Å2

Number of
H-Bond Acceptors:	24
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	5
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	22

Mass center Coordinates

X	Y	Z
19.3935	-7.75024	11.4471

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
O33	CZ	ARG- 35	3.8	0	Ionic (Protein Cationic)	false
O33	NH2	ARG- 35	3.11	136.84	H-Bond (Protein Donor)	false
C5'	CZ	PHE- 105	4	0	Hydrophobic	false
CPB	CZ	PHE- 105	4.17	0	Hydrophobic	false
CP8	CE1	PHE- 105	4.28	0	Hydrophobic	false
N6	O	GLY- 141	3.36	167.35	H-Bond (Ligand Donor)	false
NP1	O	GLY- 141	3.09	127.81	H-Bond (Ligand Donor)	false
N6	O	ALA- 143	2.69	151.03	H-Bond (Ligand Donor)	false
OS1	N	ALA- 143	2.96	150.63	H-Bond (Protein Donor)	false
N1	N	ILE- 145	2.96	165.28	H-Bond (Protein Donor)	false
CP9	CB	PRO- 178	4.1	0	Hydrophobic	false
CP8	CB	PRO- 178	3.98	0	Hydrophobic	false
CP4	CB	ALA- 180	4.25	0	Hydrophobic	false
OS4	N	GLY- 182	2.79	171.54	H-Bond (Protein Donor)	false
OS5	N	GLY- 414	2.95	168.66	H-Bond (Protein Donor)	false
S	CG2	VAL- 439	3.93	0	Hydrophobic	false
S	CB	MET- 440	4.13	0	Hydrophobic	false