scPDB - 2d0o entry

Protein Data Bank Entry:

PDB ID : 2d0o

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2005-08-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Diol dehydratase-reactivating factor alpha subunit
ID:	DDRFA_KLEOK
AC:	O68195
Organism:	Klebsiella oxytoca
Reign:	Bacteria
TaxID:	1006551
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	27.820
Number of residues:	46
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	1
Water Molecules:	9
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.248	469.125

% Hydrophobic	% Polar
37.41	62.59
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	65.12 %
Polar Surface area:	260.7 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
22.6808	54.0377	12.1082

Binding mode :

What is Poseview ?

2D View
3D View

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
O2B	N	ASN- 11	2.92	152.05	H-Bond (Protein Donor)	false
O1B	N	SER- 12	2.78	156.49	H-Bond (Protein Donor)	false
C5'	CB	SER- 12	3.67	0	Hydrophobic	false
O1B	N	SER- 13	2.74	175.57	H-Bond (Protein Donor)	false
O2A	OG	SER- 13	2.58	163.15	H-Bond (Protein Donor)	false
C3'	CB	ALA- 416	3.71	0	Hydrophobic	false
C4'	CB	ALA- 416	4.04	0	Hydrophobic	false
O2'	OE2	GLU- 459	2.51	158.42	H-Bond (Ligand Donor)	false
O3'	NZ	LYS- 462	3.32	123.4	H-Bond (Protein Donor)	false
O2'	NZ	LYS- 462	2.81	148.31	H-Bond (Protein Donor)	false
C2'	CD	LYS- 463	4.44	0	Hydrophobic	false
O1A	N	GLY- 557	2.73	165.37	H-Bond (Protein Donor)	false
O5'	N	GLY- 557	3.27	121.99	H-Bond (Protein Donor)	false
O4'	OG	SER- 558	3.27	163.2	H-Bond (Protein Donor)	false
O2A	NH1	ARG- 591	2.77	158.57	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 591	3.81	0	Ionic (Protein Cationic)	false
O3B	MG	MG- 1004	1.95	0	Metal Acceptor	false
O2A	O	HOH- 1007	2.97	179.97	H-Bond (Protein Donor)	false
O1A	O	HOH- 1013	3.01	154.93	H-Bond (Protein Donor)	false
O2B	O	HOH- 1032	2.57	127.94	H-Bond (Protein Donor)	false
O3'	O	HOH- 1066	2.64	163.94	H-Bond (Ligand Donor)	false
N1	O	HOH- 1099	3	162.89	H-Bond (Protein Donor)	false