scPDB - 3r5f entry

Protein Data Bank Entry:

PDB ID : 3r5f

Resolution :2.070 Å

Experimental Method : X-ray

Deposition Date : 2011-03-18

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:	Q5H614_XANOR
AC:	Q5H614
Organism:	Xanthomonas oryzae pv. oryzae
Reign:	Bacteria
TaxID:	291331
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	37.332
Number of residues:	30
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.031	826.875

% Hydrophobic	% Polar
32.65	67.35
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	53.01 %
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
6.42826	19.7507	14.0666

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
O2A	NZ	LYS- 141	3.22	165.89	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 141	3.22	0	Ionic (Protein Cationic)	false
C1'	CE2	PHE- 183	3.99	0	Hydrophobic	false
DuAr	DuAr	PHE- 183	3.5	0	Aromatic Face/Face	false
O2A	NZ	LYS- 185	2.87	163.16	H-Bond (Protein Donor)	false
N7	NZ	LYS- 185	2.78	142.25	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 185	2.87	0	Ionic (Protein Cationic)	false
O2G	OG	SER- 192	2.58	159.95	H-Bond (Protein Donor)	false
O3B	OG	SER- 192	3.48	133.44	H-Bond (Protein Donor)	false
N6	OE1	GLU- 221	2.94	160.5	H-Bond (Ligand Donor)	false
N6	O	ALA- 222	2.78	142.45	H-Bond (Ligand Donor)	false
N1	N	VAL- 224	2.71	173.8	H-Bond (Protein Donor)	false
C2'	CE1	PHE- 304	4.42	0	Hydrophobic	false
O1B	OE2	GLU- 315	2.6	156	H-Bond (Protein Donor)	false
O1A	MG	MG- 369	2.77	0	Metal Acceptor	false