scPDB - 3daa entry

Protein Data Bank Entry:

PDB ID : 3daa

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 1998-01-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	D-alanine aminotransferase
ID:	DAAA_BACYM
AC:	P19938
Organism:	Bacillus sp.
Reign:	Bacteria
TaxID:	72579
EC Number:	2.6.1.21

Chains:

Chain Name:	Percentage of Residues within binding site
A	91 %
B	9 %

Ligand binding site composition:

B-Factor:	11.618
Number of residues:	36
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.598	752.625

% Hydrophobic	% Polar
34.98	65.02
According to VolSite

Ligand :

HET Code:	PDD
Formula:	C11H15N2O7P
Molecular weight:	318.220 g/mol
DrugBank ID:	DB01993
Buried Surface Area:	75.89 %
Polar Surface area:	172.09 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	2
Rings:	1
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
33.6684	8.31281	-9.06443

Binding mode :

What is Poseview ?

2D View
3D View

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
O	OH	TYR- 31	2.84	167.53	H-Bond (Protein Donor)	false
CA	CG2	VAL- 33	3.94	0	Hydrophobic	false
CB	CB	VAL- 33	3.93	0	Hydrophobic	false
OP2	NH2	ARG- 50	2.72	137.97	H-Bond (Protein Donor)	false
OP2	NH1	ARG- 50	3.02	127.9	H-Bond (Protein Donor)	false
OP2	CZ	ARG- 50	3.26	0	Ionic (Protein Cationic)	false
O	NH2	ARG- 98	3.29	168.06	H-Bond (Protein Donor)	false
OXT	NH1	ARG- 98	3.4	165.12	H-Bond (Protein Donor)	false
C2A	CG	GLU- 177	4.45	0	Hydrophobic	false
C4A	CB	SER- 180	4.02	0	Hydrophobic	false
C5	CD2	LEU- 201	3.8	0	Hydrophobic	false
OP2	N	ILE- 204	2.9	171.36	H-Bond (Protein Donor)	false
OP3	OG1	THR- 205	2.82	155.95	H-Bond (Protein Donor)	false
OP3	N	THR- 205	3.07	160.49	H-Bond (Protein Donor)	false
C4A	CB	SER- 240	4.36	0	Hydrophobic	false
C5A	CB	SER- 240	3.9	0	Hydrophobic	false
OP1	N	THR- 241	2.93	145.35	H-Bond (Protein Donor)	false
OP1	OG1	THR- 241	2.61	159.98	H-Bond (Protein Donor)	false
CB	CB	THR- 241	4.29	0	Hydrophobic	false
O3A	O	HOH- 675	2.96	164.46	H-Bond (Protein Donor)	false
OP1	O	HOH- 692	2.97	148.99	H-Bond (Protein Donor)	false