scPDB - 1y9d entry

Protein Data Bank Entry:

PDB ID : 1y9d

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2004-12-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pyruvate oxidase
ID:	POXB_LACPL
AC:	P37063
Organism:	Lactobacillus plantarum
Reign:	Bacteria
TaxID:	220668
EC Number:	1.2.3.3

Chains:

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

Ligand binding site composition:

B-Factor:	53.587
Number of residues:	32
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.336	418.500

% Hydrophobic	% Polar
50.81	49.19
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	59.2 %
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
59.7475	5.97333	21.739

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
C5B	CD1	ILE- 221	3.67	0	Hydrophobic	false
O2P	N	ILE- 221	3.1	153.83	H-Bond (Protein Donor)	false
O2P	OG1	THR- 244	2.59	163.04	H-Bond (Protein Donor)	false
O1A	ND2	ASN- 285	3.46	148.45	H-Bond (Protein Donor)	false
O1A	ND2	ASN- 286	2.98	137.72	H-Bond (Protein Donor)	false
O3B	OD1	ASP- 306	3.39	121.82	H-Bond (Ligand Donor)	false
O3B	OD2	ASP- 306	2.75	163.57	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 306	2.77	162.48	H-Bond (Ligand Donor)	false
N3A	N	ILE- 307	3.41	123.81	H-Bond (Protein Donor)	false
C3B	CD	LYS- 311	4.37	0	Hydrophobic	false
O3B	NZ	LYS- 311	3.38	139.6	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 311	3.07	139.78	H-Bond (Protein Donor)	false
N6A	OD1	ASP- 325	3.06	160.83	H-Bond (Ligand Donor)	false
N1A	N	ALA- 326	2.86	146.51	H-Bond (Protein Donor)	false