scPDB - 4c5c entry

Protein Data Bank Entry:

PDB ID : 4c5c

Resolution :1.400 Å

Experimental Method : X-ray

Deposition Date : 2013-09-10

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 B
ID:	DDLB_ECOLI
AC:	P07862
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	6.3.2.4

Chains:

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

Ligand binding site composition:

B-Factor:	11.383
Number of residues:	45
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	3
Water Molecules:	5
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.631	408.375

% Hydrophobic	% Polar
54.55	45.45
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	86.61 %
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
7.89832	29.745	68.2735

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
O1B	NZ	LYS- 97	2.74	176.05	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 97	2.74	0	Ionic (Protein Cationic)	false
C1'	CD1	ILE- 142	3.88	0	Hydrophobic	false
O2A	NZ	LYS- 144	2.74	160.5	H-Bond (Protein Donor)	false
N7	NZ	LYS- 144	3	165.17	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 144	2.74	0	Ionic (Protein Cationic)	false
O1G	N	SER- 150	2.9	134.25	H-Bond (Protein Donor)	false
O3G	N	SER- 150	3.45	165.32	H-Bond (Protein Donor)	false
O2B	N	SER- 151	2.78	144.09	H-Bond (Protein Donor)	false
C5'	CB	SER- 151	4.37	0	Hydrophobic	false
C5'	SD	MET- 154	3.63	0	Hydrophobic	false
C4'	CE	MET- 154	3.99	0	Hydrophobic	false
C1'	CE	MET- 154	4.32	0	Hydrophobic	false
N6	OE1	GLU- 180	2.94	168.63	H-Bond (Ligand Donor)	false
N6	O	LYS- 181	2.92	160.44	H-Bond (Ligand Donor)	false
N1	N	LEU- 183	2.89	173.04	H-Bond (Protein Donor)	false
O2'	OE1	GLU- 187	2.66	164.79	H-Bond (Ligand Donor)	false
C4'	CD2	PHE- 209	4.14	0	Hydrophobic	false
C1'	CB	PHE- 209	4.01	0	Hydrophobic	false
O2'	N	TYR- 210	3	159.93	H-Bond (Protein Donor)	false
C2'	CB	TYR- 210	4.33	0	Hydrophobic	false
O1G	NZ	LYS- 215	2.72	163.41	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 215	2.72	0	Ionic (Protein Cationic)	false
O2G	NZ	LYS- 215	3.56	0	Ionic (Protein Cationic)	false
O2G	NH2	ARG- 255	2.95	132.1	H-Bond (Protein Donor)	false
C2'	SD	MET- 259	4.15	0	Hydrophobic	false
C3'	CD1	LEU- 269	3.89	0	Hydrophobic	false
O2G	ND2	ASN- 272	3.5	120.04	H-Bond (Protein Donor)	false
O1G	N	DAL- 311	3.43	126.31	H-Bond (Protein Donor)	false
O3G	N	DAL- 311	2.8	171.7	H-Bond (Protein Donor)	false
O1G	N	DAL- 311	3.43	0	Ionic (Protein Cationic)	false
O3G	N	DAL- 311	2.8	0	Ionic (Protein Cationic)	false
O3G	MG	MG- 1313	1.96	0	Metal Acceptor	false
O1B	MG	MG- 1313	2.02	0	Metal Acceptor	false
O2G	MG	MG- 1314	2.03	0	Metal Acceptor	false
O3B	MG	MG- 1314	2.19	0	Metal Acceptor	false
O1A	MG	MG- 1314	1.97	0	Metal Acceptor	false