scPDB - 2dji entry

Protein Data Bank Entry:

PDB ID : 2dji

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2006-04-03

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:	A9X9K8_9LACT
AC:	A9X9K8
Organism:	Aerococcus viridans
Reign:	Bacteria
TaxID:	1377
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	21.209
Number of residues:	56
Including
Standard Amino Acids:	53
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.460	1235.250

% Hydrophobic	% Polar
51.91	48.09
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	68 %
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
26.5559	21.2697	14.0774

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
C5B	CG1	ILE- 216	3.64	0	Hydrophobic	false
O2P	N	ILE- 216	2.77	151.13	H-Bond (Protein Donor)	false
O5'	OG1	THR- 239	3.26	127.12	H-Bond (Protein Donor)	false
O2P	OG1	THR- 239	2.62	164.18	H-Bond (Protein Donor)	false
C4'	CB	THR- 239	4.31	0	Hydrophobic	false
N1	N	GLY- 240	3.47	135.14	H-Bond (Protein Donor)	false
O2	N	GLY- 240	3.15	146.13	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 241	2.71	161.56	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 241	2.71	0	Ionic (Protein Cationic)	false
C3'	CD	LYS- 241	4.23	0	Hydrophobic	false
C4'	CG	LYS- 241	3.7	0	Hydrophobic	false
C5'	CD	LYS- 241	3.48	0	Hydrophobic	false
N3	O	THR- 257	2.82	164.46	H-Bond (Ligand Donor)	false
O4	N	VAL- 260	2.54	130.55	H-Bond (Protein Donor)	false
C6	CG2	VAL- 260	3.39	0	Hydrophobic	false
O1P	OG	SER- 280	2.64	155.79	H-Bond (Protein Donor)	false
C3B	CB	ASN- 281	4.35	0	Hydrophobic	false
O1P	N	ASN- 281	2.89	158.07	H-Bond (Protein Donor)	false
C3'	CG	PRO- 283	3.85	0	Hydrophobic	false
C2'	CE2	PHE- 284	4.2	0	Hydrophobic	false
O3B	OD2	ASP- 301	2.74	166.58	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 301	2.75	166.16	H-Bond (Ligand Donor)	false
N3A	N	ILE- 302	3.48	135.67	H-Bond (Protein Donor)	false
C3B	CG	MET- 306	4.46	0	Hydrophobic	false
N6A	OD1	ASP- 320	2.95	166.1	H-Bond (Ligand Donor)	false
N1A	N	ALA- 321	2.88	153.75	H-Bond (Protein Donor)	false
C8M	CG1	VAL- 389	3.96	0	Hydrophobic	false
C8	CG	GLN- 394	4.32	0	Hydrophobic	false
C7	CG	GLN- 394	4.01	0	Hydrophobic	false
C1'	CB	PRO- 412	4.16	0	Hydrophobic	false
C3'	CB	PRO- 412	4.41	0	Hydrophobic	false
O2'	O	PRO- 412	2.77	162.75	H-Bond (Ligand Donor)	false
C8M	CB	ALA- 415	3.5	0	Hydrophobic	false
C7M	CZ	PHE- 474	4.48	0	Hydrophobic	false
O2	O	HOH- 1692	2.76	179.98	H-Bond (Protein Donor)	false