scPDB - 5i39 entry

Protein Data Bank Entry:

PDB ID : 5i39

Resolution :1.200 Å

Experimental Method : X-ray

Deposition Date : 2016-02-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	L-amino acid deaminase
ID:	Q9LCB2_PROVU
AC:	Q9LCB2
Organism:	Proteus vulgaris
Reign:	Bacteria
TaxID:	585
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	10.365
Number of residues:	70
Including
Standard Amino Acids:	64
Non Standard Amino Acids:	0
Water Molecules:	6
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.880	398.250

% Hydrophobic	% Polar
52.54	47.46
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	81.62 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
43.8232	50.0827	13.8615

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
C4'	CG2	ILE- 64	3.97	0	Hydrophobic	false
O1P	N	LEU- 65	3.1	159.76	H-Bond (Protein Donor)	false
O3B	OE2	GLU- 84	3.19	127.64	H-Bond (Ligand Donor)	false
O3B	OE1	GLU- 84	2.68	171.43	H-Bond (Ligand Donor)	false
O2B	OE2	GLU- 84	2.67	146.98	H-Bond (Ligand Donor)	false
O2B	NZ	LYS- 85	3.1	144.23	H-Bond (Protein Donor)	false
N3A	N	LYS- 85	3.07	144.17	H-Bond (Protein Donor)	false
C2B	CG	LYS- 85	4.29	0	Hydrophobic	false
C3B	CG	GLU- 91	3.9	0	Hydrophobic	false
O1A	N	GLN- 92	3.1	153.81	H-Bond (Protein Donor)	false
C8M	CG	GLN- 92	4.16	0	Hydrophobic	false
C4'	CB	GLN- 92	4.08	0	Hydrophobic	false
O2A	OG	SER- 93	2.56	159.38	H-Bond (Protein Donor)	false
O2A	N	SER- 93	2.91	137.16	H-Bond (Protein Donor)	false
O4'	OG	SER- 93	2.88	151.38	H-Bond (Ligand Donor)	false
C6	CB	PHE- 96	3.94	0	Hydrophobic	false
C9A	CB	PHE- 96	3.65	0	Hydrophobic	false
N5	N	TYR- 97	3.15	169.66	H-Bond (Protein Donor)	false
C6	CB	TYR- 97	4.41	0	Hydrophobic	false
O4	N	GLY- 98	2.97	149.97	H-Bond (Protein Donor)	false
N3	O	GLN- 99	2.84	169.55	H-Bond (Ligand Donor)	false
O4	N	GLN- 99	3.04	162.94	H-Bond (Protein Donor)	false
N6A	O	ALA- 227	2.95	169.43	H-Bond (Ligand Donor)	false
N1A	N	ALA- 227	2.92	155.44	H-Bond (Protein Donor)	false
C2B	CZ3	TRP- 259	3.94	0	Hydrophobic	false
C7M	CB	GLN- 278	3.88	0	Hydrophobic	false
C7M	CG	GLN- 280	3.84	0	Hydrophobic	false
C7	CE	MET- 411	4.01	0	Hydrophobic	false
C8M	CG	MET- 411	3.48	0	Hydrophobic	false
C9	SD	MET- 411	3.7	0	Hydrophobic	false
O3'	O	THR- 436	2.76	137.2	H-Bond (Ligand Donor)	false
O3'	N	GLY- 439	2.84	138.77	H-Bond (Protein Donor)	false
C2'	CG	MET- 440	4.11	0	Hydrophobic	false
O2	N	THR- 441	2.93	158.78	H-Bond (Protein Donor)	false
O2	OG1	THR- 441	2.74	155.59	H-Bond (Protein Donor)	false
O1A	O	HOH- 610	2.61	166.86	H-Bond (Protein Donor)	false
O2P	O	HOH- 611	2.62	149.22	H-Bond (Protein Donor)	false
O1P	O	HOH- 620	2.65	179.95	H-Bond (Protein Donor)	false