scPDB - 3axk entry

Protein Data Bank Entry:

PDB ID : 3axk

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2011-04-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ribulose bisphosphate carboxylase large chain
ID:	RBL_ORYSJ
AC:	P0C512
Organism:	Oryza sativa subsp. japonica
Reign:	Eukaryota
TaxID:	39947
EC Number:	4.1.1.39

Chains:

Chain Name:	Percentage of Residues within binding site
A	72 %
B	28 %

Ligand binding site composition:

B-Factor:	24.352
Number of residues:	46
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	2
Water Molecules:	3
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.535	867.375

% Hydrophobic	% Polar
22.96	77.04
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	39.34 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
29.0138	22.8781	-21.07

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
N6A	OE2	GLU- 60	2.65	150.43	H-Bond (Ligand Donor)	false
O1A	NZ	LYS- 175	3.43	133.03	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 175	3.18	159.54	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 175	3.43	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 175	3.18	0	Ionic (Protein Cationic)	false
O2X	NH2	ARG- 295	2.61	146.29	H-Bond (Protein Donor)	false
O2X	NE	ARG- 295	2.79	139.01	H-Bond (Protein Donor)	false
O2X	CZ	ARG- 295	3.11	0	Ionic (Protein Cationic)	false
O3X	NE2	HIS- 298	2.56	172.32	H-Bond (Protein Donor)	false
C5B	CB	SER- 379	4	0	Hydrophobic	false
O1N	N	GLY- 381	2.86	141.79	H-Bond (Protein Donor)	false
O2N	N	GLY- 381	2.67	131.31	H-Bond (Protein Donor)	false
O5D	N	GLY- 404	3.34	153.59	H-Bond (Protein Donor)	false
O2N	O	HOH- 580	2.76	179.95	H-Bond (Protein Donor)	false
O2X	O	HOH- 595	2.91	179.96	H-Bond (Protein Donor)	false