scPDB - 2z02 entry

Protein Data Bank Entry:

PDB ID : 2z02

Resolution :2.030 Å

Experimental Method : X-ray

Deposition Date : 2007-05-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Phosphoribosylaminoimidazole-succinocarboxamide synthase
ID:	PUR7_METJA
AC:	Q58987
Organism:	Methanocaldococcus jannaschii
Reign:	Archaea
TaxID:	243232
EC Number:	6.3.2.6

Chains:

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

Ligand binding site composition:

B-Factor:	27.230
Number of residues:	28
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.651	1279.125

% Hydrophobic	% Polar
31.13	68.87
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	66.87 %
Polar Surface area:	319.88 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-3.37774	33.0028	11.5766

Binding mode :

What is Poseview ?

2D View
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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
O2B	OH	TYR- 15	2.87	169.57	H-Bond (Protein Donor)	false
C4'	CE2	TYR- 15	3.64	0	Hydrophobic	false
O2G	NZ	LYS- 18	3.48	0	Ionic (Protein Cationic)	false
O1B	NZ	LYS- 18	3.24	0	Ionic (Protein Cationic)	false
O1B	NZ	LYS- 18	3.24	174.59	H-Bond (Protein Donor)	false
O1B	N	LYS- 18	3.03	145.51	H-Bond (Protein Donor)	false
O1A	N	ALA- 19	2.74	163.34	H-Bond (Protein Donor)	false
O1A	N	LYS- 20	2.7	165.82	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 20	2.79	167.47	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 20	2.79	0	Ionic (Protein Cationic)	false
C5'	CB	LYS- 20	4.03	0	Hydrophobic	false
C5'	CD1	ILE- 22	4.48	0	Hydrophobic	false
C4'	CG1	ILE- 22	4.21	0	Hydrophobic	false
C1'	CD1	ILE- 22	4.22	0	Hydrophobic	false
N6	ND1	HIS- 75	2.8	155.67	H-Bond (Ligand Donor)	false
N6	O	LYS- 88	3.01	159.24	H-Bond (Ligand Donor)	false
N1	N	VAL- 90	3.36	169.03	H-Bond (Protein Donor)	false
C2'	CG1	ILE- 92	4.23	0	Hydrophobic	false
O2G	NZ	LYS- 129	3.81	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 129	3.55	0	Ionic (Protein Cationic)	false
O2'	OE1	GLU- 185	3.02	153.77	H-Bond (Ligand Donor)	false
N7	N	ASP- 198	3.37	136.41	H-Bond (Protein Donor)	false