scPDB - 1p0y entry

Protein Data Bank Entry:

PDB ID : 1p0y

Resolution :2.550 Å

Experimental Method : X-ray

Deposition Date : 2003-04-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic
ID:	RBCMT_PEA
AC:	Q43088
Organism:	Pisum sativum
Reign:	Eukaryota
TaxID:	3888
EC Number:	2.1.1.127

Chains:

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

Ligand binding site composition:

B-Factor:	56.219
Number of residues:	31
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.649	550.125

% Hydrophobic	% Polar
38.65	61.35
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	66.89 %
Polar Surface area:	212.38 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
117.706	128.141	141.499

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
N	O	GLU- 80	2.94	129.15	H-Bond (Ligand Donor)	false
N	O	LEU- 82	2.88	138.22	H-Bond (Ligand Donor)	false
OXT	N	LEU- 82	2.84	157.32	H-Bond (Protein Donor)	false
SD	CG	ARG- 222	4.09	0	Hydrophobic	false
O	CZ	ARG- 222	3.53	0	Ionic (Protein Cationic)	false
N	OD1	ASN- 242	2.77	159.48	H-Bond (Ligand Donor)	false
N7	N	HIS- 243	2.89	179.15	H-Bond (Protein Donor)	false
N6	O	HIS- 243	2.72	140.3	H-Bond (Ligand Donor)	false
C5'	CE1	TYR- 287	4.08	0	Hydrophobic	false
C3'	CB	TYR- 300	3.78	0	Hydrophobic	false
C2'	CD2	PHE- 302	4.43	0	Hydrophobic	false
O2'	O	HOH- 909	2.6	179.97	H-Bond (Protein Donor)	false