scPDB - 3a13 entry

Protein Data Bank Entry:

PDB ID : 3a13

Resolution :2.340 Å

Experimental Method : X-ray

Deposition Date : 2009-03-25

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
ID:	RBL_THEKO
AC:	O93627
Organism:	Thermococcus kodakarensis )
Reign:	Archaea
TaxID:	69014
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	25.447
Number of residues:	34
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	2
Water Molecules:	3
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.537	769.500

% Hydrophobic	% Polar
51.32	48.68
According to VolSite

Ligand :

HET Code:	CAP
Formula:	C6H9O13P2
Molecular weight:	351.075 g/mol
DrugBank ID:	-
Buried Surface Area:	68.62 %
Polar Surface area:	265.27 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	3
Rings:	0
Aromatic rings:	0
Anionic atoms:	5
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
20.2267	34.8057	93.9392

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
O1	NZ	LYS- 163	3.41	125.36	H-Bond (Protein Donor)	false
O2	NZ	LYS- 163	3.06	159.24	H-Bond (Protein Donor)	false
O7	NZ	LYS- 163	3	0	Ionic (Protein Cationic)	false
O7	NZ	LYS- 165	2.79	0	Ionic (Protein Cationic)	false
O3	OQ2	KCX- 189	2.63	143.78	H-Bond (Ligand Donor)	false
O3	NE2	HIS- 281	2.75	172.12	H-Bond (Protein Donor)	false
O4P	CZ	ARG- 282	3.77	0	Ionic (Protein Cationic)	false
O5P	CZ	ARG- 282	3.69	0	Ionic (Protein Cationic)	false
O4P	NE	ARG- 282	2.86	167.61	H-Bond (Protein Donor)	false
O5P	NH2	ARG- 282	2.85	160.96	H-Bond (Protein Donor)	false
O6P	ND1	HIS- 314	2.83	156.3	H-Bond (Protein Donor)	false
O6	NZ	LYS- 322	2.86	156.18	H-Bond (Protein Donor)	false
O3P	NZ	LYS- 322	2.67	144.31	H-Bond (Protein Donor)	false
O6	NZ	LYS- 322	2.86	0	Ionic (Protein Cationic)	false
O3P	NZ	LYS- 322	2.67	0	Ionic (Protein Cationic)	false
C4	CD1	LEU- 323	3.97	0	Hydrophobic	false
O4	OG	SER- 367	3.2	154.56	H-Bond (Protein Donor)	false
O3P	N	GLY- 369	2.72	163.57	H-Bond (Protein Donor)	false
O1P	NE2	GLN- 389	3.47	144.78	H-Bond (Protein Donor)	false
O1P	N	GLY- 391	3.12	150.87	H-Bond (Protein Donor)	false
O2P	N	GLY- 392	3.04	152.61	H-Bond (Protein Donor)	false
O2	MG	MG- 445	2.1	0	Metal Acceptor	false
O3	MG	MG- 445	2.17	0	Metal Acceptor	false
O6P	O	HOH- 528	2.67	165.46	H-Bond (Protein Donor)	false