scPDB - 2x3j entry

Protein Data Bank Entry:

PDB ID : 2x3j

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2010-01-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	AcsD
ID:	Q93AT8_DICCH
AC:	Q93AT8
Organism:	Dickeya chrysanthemi
Reign:	Bacteria
TaxID:	556
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	32.881
Number of residues:	44
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	1
Water Molecules:	7
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.885	1380.375

% Hydrophobic	% Polar
35.21	64.79
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	70.55 %
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
-5.33419	-8.36819	-32.2437

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
O2G	OG	SER- 279	2.79	157.45	H-Bond (Protein Donor)	false
O3B	OG	SER- 279	3.24	129.4	H-Bond (Protein Donor)	false
C4'	CB	SER- 279	4.3	0	Hydrophobic	false
O1B	CZ	ARG- 281	3.23	0	Ionic (Protein Cationic)	false
O2B	CZ	ARG- 281	3.84	0	Ionic (Protein Cationic)	false
O1B	NH2	ARG- 281	2.83	141.65	H-Bond (Protein Donor)	false
O1B	NE	ARG- 281	2.79	146.86	H-Bond (Protein Donor)	false
O2G	OG1	THR- 282	2.88	156.29	H-Bond (Protein Donor)	false
O3G	NZ	LYS- 293	2.74	169.48	H-Bond (Protein Donor)	false
O3G	NZ	LYS- 293	2.74	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 293	2.96	0	Ionic (Protein Cationic)	false
C3'	CG2	ILE- 300	4.48	0	Hydrophobic	false
C2'	CG2	THR- 301	4.3	0	Hydrophobic	false
O2'	OG1	THR- 301	2.68	157.51	H-Bond (Ligand Donor)	false
O2G	NH1	ARG- 369	3.05	155.51	H-Bond (Protein Donor)	false
O3G	NH1	ARG- 369	2.95	129.11	H-Bond (Protein Donor)	false
O3G	CZ	ARG- 369	3.12	0	Ionic (Protein Cationic)	false
O1A	NE2	HIS- 444	3	134.09	H-Bond (Protein Donor)	false
O1G	NE2	GLN- 446	2.77	157.16	H-Bond (Protein Donor)	false
C5'	CB	GLN- 446	4.18	0	Hydrophobic	false
C4'	CG	GLN- 446	3.98	0	Hydrophobic	false
C1'	CG	GLN- 446	4.11	0	Hydrophobic	false
O1A	ND2	ASN- 447	3.46	124.64	H-Bond (Protein Donor)	false
N1	ND2	ASN- 509	2.99	170.61	H-Bond (Protein Donor)	false
O1G	MG	MG- 1589	2.13	0	Metal Acceptor	false
O1A	MG	MG- 1589	2.24	0	Metal Acceptor	false
O3A	MG	MG- 1589	2.43	0	Metal Acceptor	false
O2'	O	HOH- 2080	3.11	179.95	H-Bond (Protein Donor)	false
O1A	O	HOH- 2208	3	156.52	H-Bond (Protein Donor)	false
O2A	O	HOH- 2262	2.66	179.96	H-Bond (Protein Donor)	false