scPDB - 2i8c entry

Protein Data Bank Entry:

PDB ID : 2i8c

Resolution :2.460 Å

Experimental Method : X-ray

Deposition Date : 2006-09-01

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_STAAC
AC:	Q5HEB7
Organism:	Staphylococcus aureus
Reign:	Bacteria
TaxID:	93062
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	57.364
Number of residues:	26
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.267	702.000

% Hydrophobic	% Polar
48.56	51.44
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	54.48 %
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
20.6573	14.4509	33.6448

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
DuAr	DuAr	PHE- 175	3.76	0	Aromatic Face/Face	false
O1A	NZ	LYS- 177	3.07	150.28	H-Bond (Protein Donor)	false
N7	NZ	LYS- 177	2.86	136.93	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 177	3.07	0	Ionic (Protein Cationic)	false
O2B	OG	SER- 183	3.34	143.79	H-Bond (Protein Donor)	false
N6	O	GLN- 214	3.03	154.32	H-Bond (Ligand Donor)	false
N1	N	VAL- 216	3.05	170.22	H-Bond (Protein Donor)	false
C2'	CZ	PHE- 295	4.3	0	Hydrophobic	false
O1A	ND2	ASN- 305	3.07	158.11	H-Bond (Protein Donor)	false
O2A	ND2	ASN- 305	3.04	125.07	H-Bond (Protein Donor)	false
O2B	MG	MG- 402	2.1	0	Metal Acceptor	false
O2A	MG	MG- 402	2.21	0	Metal Acceptor	false