scPDB - 2buf entry

Protein Data Bank Entry:

PDB ID : 2buf

Resolution :2.950 Å

Experimental Method : X-ray

Deposition Date : 2005-06-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Acetylglutamate kinase
ID:	ARGB_PSEAE
AC:	Q9HTN2
Organism:	Pseudomonas aeruginosa
Reign:	Bacteria
TaxID:	208964
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
C	12 %
I	88 %

Ligand binding site composition:

B-Factor:	66.065
Number of residues:	34
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.346	479.250

% Hydrophobic	% Polar
45.07	54.93
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	62.38 %
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
-23.7047	29.747	-37.3622

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
O1B	NZ	LYS- 33	3.33	0	Ionic (Protein Cationic)	false
C2'	CG	PRO- 70	4.28	0	Hydrophobic	false
O2B	OG1	THR- 218	2.52	167.19	H-Bond (Protein Donor)	false
C3'	CG2	ILE- 220	4.37	0	Hydrophobic	false
N6	O	MET- 224	2.92	144.45	H-Bond (Ligand Donor)	false
N1	N	MET- 224	2.66	165.96	H-Bond (Protein Donor)	false
N6	O	THR- 247	2.99	134.89	H-Bond (Ligand Donor)	false
C2'	CZ	TYR- 249	4.34	0	Hydrophobic	false
C1'	CE1	TYR- 249	4.06	0	Hydrophobic	false
O2'	OH	TYR- 249	3.24	165.35	H-Bond (Ligand Donor)	false
N7	N	TYR- 249	3.21	166.56	H-Bond (Protein Donor)	false
C5'	CE	MET- 252	4.48	0	Hydrophobic	false
C1'	CB	MET- 252	4.27	0	Hydrophobic	false
O1B	NZ	LYS- 255	3.43	120.61	H-Bond (Protein Donor)	false
O5'	NZ	LYS- 255	3.5	147.4	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 255	3.43	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 255	2.66	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 255	3.79	0	Ionic (Protein Cationic)	false
O1B	MG	MG- 1299	2.45	0	Metal Acceptor	false