scPDB - 1j0d entry

Protein Data Bank Entry:

PDB ID : 1j0d

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2002-11-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	1-aminocyclopropane-1-carboxylate deaminase
ID:	1A1D_CYBSA
AC:	Q7M523
Organism:	Cyberlindnera saturnus
Reign:	Eukaryota
TaxID:	907340
EC Number:	3.5.99.7

Chains:

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

Ligand binding site composition:

B-Factor:	42.430
Number of residues:	46
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.133	263.250

% Hydrophobic	% Polar
37.18	62.82
According to VolSite

Ligand :

HET Code:	5PA
Formula:	C12H15N2O7P
Molecular weight:	330.230 g/mol
DrugBank ID:	DB02849
Buried Surface Area:	79.87 %
Polar Surface area:	172.09 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	2
Rings:	2
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
9.49782	110.045	29.9273

Binding mode :

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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
O2P	NZ	LYS- 54	2.9	166.82	H-Bond (Protein Donor)	false
O2P	NZ	LYS- 54	2.9	0	Ionic (Protein Cationic)	false
O7	OG	SER- 78	3.25	160.19	H-Bond (Protein Donor)	false
O7	N	GLN- 80	2.53	148.84	H-Bond (Protein Donor)	false
C9	CB	GLN- 80	4.03	0	Hydrophobic	false
O1P	N	VAL- 201	3.05	159.6	H-Bond (Protein Donor)	false
C5A	CG1	VAL- 201	3.53	0	Hydrophobic	false
O3P	N	THR- 202	2.96	140.53	H-Bond (Protein Donor)	false
C10	CG2	THR- 202	4.17	0	Hydrophobic	false
O1P	N	GLY- 203	3.46	150.39	H-Bond (Protein Donor)	false
O2P	OG	SER- 204	3.3	145.23	H-Bond (Protein Donor)	false
O2P	N	THR- 205	2.8	154.06	H-Bond (Protein Donor)	false
O4P	OG1	THR- 205	3.33	134.48	H-Bond (Protein Donor)	false
C5A	CD2	TYR- 295	4.01	0	Hydrophobic	false
C5	CB	TYR- 295	4.45	0	Hydrophobic	false
C2A	CB	TYR- 295	3.9	0	Hydrophobic	false
C3	CB	TYR- 295	4.32	0	Hydrophobic	false
C10	CZ	TYR- 295	4.08	0	Hydrophobic	false
DuAr	DuAr	TYR- 295	3.68	0	Aromatic Face/Face	false
N1	OE1	GLU- 296	2.64	171.05	H-Bond (Ligand Donor)	false
C2A	CG	GLU- 296	3.68	0	Hydrophobic	false
C5	CD1	LEU- 323	4.2	0	Hydrophobic	false
C2A	CB	LEU- 323	3.85	0	Hydrophobic	false