scPDB - 2zdg entry

Protein Data Bank Entry:

PDB ID : 2zdg

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2007-11-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	D-alanine--D-alanine ligase
ID:	DDL_THET8
AC:	Q5SHZ3
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	300852
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	43.235
Number of residues:	27
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.388	860.625

% Hydrophobic	% Polar
37.65	62.35
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	59.27 %
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
22.3619	68.6725	29.1616

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
O3B	NZ	LYS- 116	3	138.93	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 116	3.22	159	H-Bond (Protein Donor)	false
O3B	NZ	LYS- 116	3	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 116	3.22	0	Ionic (Protein Cationic)	false
C1'	CE2	PHE- 151	3.48	0	Hydrophobic	false
DuAr	DuAr	PHE- 151	3.91	0	Aromatic Face/Face	false
O1A	NZ	LYS- 153	3.02	149.67	H-Bond (Protein Donor)	false
N7	NZ	LYS- 153	3.09	176.85	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 153	3.02	0	Ionic (Protein Cationic)	false
O1B	N	SER- 160	2.85	129.25	H-Bond (Protein Donor)	false
C5'	CB	SER- 160	4.05	0	Hydrophobic	false
C5'	CD1	ILE- 163	3.85	0	Hydrophobic	false
N6	OE1	GLU- 189	3.15	170.31	H-Bond (Ligand Donor)	false
N6	O	LYS- 190	2.89	134.36	H-Bond (Ligand Donor)	false
N1	N	LEU- 192	2.62	165.84	H-Bond (Protein Donor)	false
O3'	OE1	GLU- 197	2.64	166.27	H-Bond (Ligand Donor)	false
O3'	OE2	GLU- 197	3.49	136.39	H-Bond (Ligand Donor)	false
O2'	OE1	GLU- 197	2.59	159.78	H-Bond (Ligand Donor)	false
C3'	CZ	PHE- 272	4.16	0	Hydrophobic	false
C2'	CE1	PHE- 272	3.89	0	Hydrophobic	false
C1'	CZ	PHE- 272	4.46	0	Hydrophobic	false
O1A	ND2	ASN- 281	3.09	176.49	H-Bond (Protein Donor)	false