scPDB - 1o69 entry

Protein Data Bank Entry:

PDB ID : 1o69

Resolution :1.840 Å

Experimental Method : X-ray

Deposition Date : 2003-10-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Aminotransferase DegT
ID:	Q9S5Y7_CAMJU
AC:	Q9S5Y7
Organism:	Campylobacter jejuni
Reign:	Bacteria
TaxID:	197
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	6 %
B	94 %

Ligand binding site composition:

B-Factor:	20.776
Number of residues:	35
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.096	266.625

% Hydrophobic	% Polar
39.24	60.76
According to VolSite

Ligand :

HET Code:	X04
Formula:	C8H9N2O6P
Molecular weight:	260.141 g/mol
DrugBank ID:	-
Buried Surface Area:	74.6 %
Polar Surface area:	158.44 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	2
Rings:	1
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
58.7724	56.8199	-8.90712

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
OP2	N	ALA- 56	2.89	178.9	H-Bond (Protein Donor)	false
C5A	CB	ALA- 56	3.7	0	Hydrophobic	false
OP1	OG1	THR- 57	2.91	157.71	H-Bond (Protein Donor)	false
OP1	N	THR- 57	3.02	149.62	H-Bond (Protein Donor)	false
C5A	CD2	PHE- 82	4.36	0	Hydrophobic	false
C2A	CB	PHE- 82	4.47	0	Hydrophobic	false
C3	CB	PHE- 82	4.02	0	Hydrophobic	false
C4A	CD2	PHE- 82	3.29	0	Hydrophobic	false
C5A	CB	ALA- 84	3.59	0	Hydrophobic	false
C2A	CG2	THR- 129	3.67	0	Hydrophobic	false
C2A	CB	ALA- 157	4.26	0	Hydrophobic	false
C5	CB	ALA- 157	3.45	0	Hydrophobic	false
C4	CB	ALA- 157	3.61	0	Hydrophobic	false
C2A	CG	GLU- 158	3.92	0	Hydrophobic	false
C3	CG	GLU- 158	4.11	0	Hydrophobic	false
OP2	OG	SER- 179	2.86	154.82	H-Bond (Protein Donor)	false
OP1	ND2	ASN- 227	3.12	161.06	H-Bond (Protein Donor)	false
OP2	O	HOH- 510	2.96	179.97	H-Bond (Protein Donor)	false
O1	O	HOH- 671	2.87	154.76	H-Bond (Protein Donor)	false