scPDB - 1knr entry

Protein Data Bank Entry:

PDB ID : 1knr

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2001-12-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	L-aspartate oxidase
ID:	NADB_ECOLI
AC:	P10902
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	1.4.3.16

Chains:

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

Ligand binding site composition:

B-Factor:	81.653
Number of residues:	72
Including
Standard Amino Acids:	71
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	CL

Cavity properties

Ligandability	Volume (Å3)
1.012	1015.875

% Hydrophobic	% Polar
44.85	55.15
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	77.08 %
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
68.5803	45.073	135.39

Binding mode :

What is Poseview ?

2D View
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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
O3B	N	SER- 16	3.24	172.21	H-Bond (Protein Donor)	false
O1P	N	ALA- 19	3.18	162.92	H-Bond (Protein Donor)	false
O2B	N	LYS- 38	3.28	140.89	H-Bond (Protein Donor)	false
O1A	N	SER- 45	2.65	160.93	H-Bond (Protein Donor)	false
O1A	OG	SER- 45	3.37	130.92	H-Bond (Protein Donor)	false
C8M	CB	SER- 45	4.06	0	Hydrophobic	false
C9	CB	SER- 45	4.35	0	Hydrophobic	false
C3'	CB	SER- 45	4.3	0	Hydrophobic	false
C5'	CB	SER- 45	4.4	0	Hydrophobic	false
O2A	N	THR- 46	2.92	142.76	H-Bond (Protein Donor)	false
O4'	OG1	THR- 46	2.94	144.59	H-Bond (Ligand Donor)	false
C7M	CB	TYR- 48	3.91	0	Hydrophobic	false
C6	CB	ALA- 49	4.37	0	Hydrophobic	false
C9A	CB	ALA- 49	4.37	0	Hydrophobic	false
N5	N	GLN- 50	3.3	153.34	H-Bond (Protein Donor)	false
C6	CG	GLN- 50	4.41	0	Hydrophobic	false
N3	O	GLY- 52	2.96	161.75	H-Bond (Ligand Donor)	false
O4	N	GLY- 52	2.97	155.37	H-Bond (Protein Donor)	false
N1A	N	ALA- 162	2.89	171.03	H-Bond (Protein Donor)	false
C8M	CB	THR- 215	4.46	0	Hydrophobic	false
C2B	CG2	ILE- 219	3.66	0	Hydrophobic	false
N6A	OD2	ASP- 223	2.75	155.02	H-Bond (Ligand Donor)	false
C7M	CD2	LEU- 257	3.5	0	Hydrophobic	false
C1'	CD1	TYR- 352	4.25	0	Hydrophobic	false
C3'	CE1	TYR- 352	4.29	0	Hydrophobic	false
O3'	OE1	GLU- 375	2.94	161.31	H-Bond (Ligand Donor)	false
C5'	CB	GLU- 375	4.04	0	Hydrophobic	false
O2P	N	GLU- 375	3.14	171.85	H-Bond (Protein Donor)	false
N1	OG	SER- 391	2.61	145.34	H-Bond (Protein Donor)	false
C1'	CB	SER- 391	3.92	0	Hydrophobic	false
C2'	CG	LEU- 392	4.37	0	Hydrophobic	false
C4'	CD2	LEU- 392	4.37	0	Hydrophobic	false
C4'	SG	CYS- 395	4.27	0	Hydrophobic	false