scPDB - 2h21 entry

Protein Data Bank Entry:

PDB ID : 2h21

Resolution :2.450 Å

Experimental Method : X-ray

Deposition Date : 2006-05-17

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:	52.026
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.131	1150.875

% Hydrophobic	% Polar
38.42	61.58
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	64.42 %
Polar Surface area:	189.77 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
118.656	129.275	140.24

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	3.03	134.65	H-Bond (Ligand Donor)	false
N	O	LEU- 82	2.83	143.84	H-Bond (Ligand Donor)	false
O	N	LEU- 82	2.64	154.76	H-Bond (Protein Donor)	false
OXT	NH2	ARG- 222	2.51	123.5	H-Bond (Protein Donor)	false
OXT	CZ	ARG- 222	3.75	0	Ionic (Protein Cationic)	false
CE	CB	ARG- 222	4.27	0	Hydrophobic	false
CE	CB	ASP- 239	4.27	0	Hydrophobic	false
N	OD1	ASN- 242	2.58	155.73	H-Bond (Ligand Donor)	false
N7	N	HIS- 243	2.89	170.38	H-Bond (Protein Donor)	false
N6	O	HIS- 243	2.68	139.45	H-Bond (Ligand Donor)	false
CE	CZ	TYR- 287	3.97	0	Hydrophobic	false
C5'	CE1	TYR- 287	3.86	0	Hydrophobic	false
C5'	CD2	TYR- 300	4.5	0	Hydrophobic	false
C3'	CB	TYR- 300	3.85	0	Hydrophobic	false
O3'	N	GLY- 301	3.5	148.02	H-Bond (Protein Donor)	false
C2'	CD2	PHE- 302	4.36	0	Hydrophobic	false
DuAr	DuAr	PHE- 302	3.9	0	Aromatic Face/Face	false
O2'	O	HOH- 819	2.63	159.38	H-Bond (Ligand Donor)	false