scPDB - 5c1o entry

Protein Data Bank Entry:

PDB ID : 5c1o

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2015-06-15

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_YERPE
AC:	Q8ZIE7
Organism:	Yersinia pestis
Reign:	Bacteria
TaxID:	632
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	73.002
Number of residues:	27
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.876	1657.125

% Hydrophobic	% Polar
43.18	56.82
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	62.48 %
Polar Surface area:	322.68 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
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
26.2078	-10.5995	30.517

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
O1B	NZ	LYS- 97	2.9	135.08	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 97	2.9	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 97	3.7	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 144	3.01	158.89	H-Bond (Protein Donor)	false
N7	NZ	LYS- 144	2.96	162.88	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 144	3.01	0	Ionic (Protein Cationic)	false
C5'	CE	MET- 154	3.71	0	Hydrophobic	false
N6	OE2	GLU- 180	3.38	160.29	H-Bond (Ligand Donor)	false
N6	O	LYS- 181	2.98	164.28	H-Bond (Ligand Donor)	false
N1	N	LEU- 183	3.17	163.5	H-Bond (Protein Donor)	false
O3'	OE1	GLU- 187	3.27	160.28	H-Bond (Ligand Donor)	false
O3'	OE2	GLU- 187	2.54	132.97	H-Bond (Ligand Donor)	false
C1'	CD1	PHE- 209	4.42	0	Hydrophobic	false
O2'	N	TYR- 210	3.3	149.26	H-Bond (Protein Donor)	false
C4'	CB	TYR- 210	4.25	0	Hydrophobic	false
C2'	SD	MET- 259	4.05	0	Hydrophobic	false
C3'	CD1	LEU- 269	3.76	0	Hydrophobic	false
O1G	MG	MG- 403	2.21	0	Metal Acceptor	false
O2G	MG	MG- 403	2.21	0	Metal Acceptor	false
O1B	MG	MG- 403	2.18	0	Metal Acceptor	false
O1A	MG	MG- 403	2.19	0	Metal Acceptor	false