scPDB - 2e0i entry

Protein Data Bank Entry:

PDB ID : 2e0i

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2006-10-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	DNA photolyase
ID:	F9VNB1_SULTO
AC:	F9VNB1
Organism:	Sulfolobus tokodaii
Reign:	Archaea
TaxID:	273063
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	21.290
Number of residues:	48
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.599	907.875

% Hydrophobic	% Polar
48.70	51.30
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	66.98 %
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
13.7646	26.5745	-4.24691

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
C3'	CB	ARG- 8	4.38	0	Hydrophobic	false
C2'	CD	ARG- 9	4.24	0	Hydrophobic	false
C3'	CB	ARG- 9	4.23	0	Hydrophobic	false
C4'	CD	ARG- 9	4.35	0	Hydrophobic	false
N3	O	ILE- 34	2.71	168.89	H-Bond (Ligand Donor)	false
O4	N	ASP- 36	3	166.52	H-Bond (Protein Donor)	false
O2A	NE2	GLN- 39	2.72	161.23	H-Bond (Protein Donor)	false
O3'	NE2	GLN- 39	3.23	174.54	H-Bond (Protein Donor)	false
C5B	CG	GLN- 39	3.7	0	Hydrophobic	false
C6	CB	GLN- 39	4.03	0	Hydrophobic	false
C6	CD2	LEU- 40	4.02	0	Hydrophobic	false
O2B	OD1	ASN- 43	2.58	162.04	H-Bond (Ligand Donor)	false
C2B	CB	TYR- 45	4.15	0	Hydrophobic	false
DuAr	DuAr	TYR- 45	3.47	0	Aromatic Face/Face	false
C7M	CG	LYS- 46	3.77	0	Hydrophobic	false
C8M	CB	ALA- 50	4.22	0	Hydrophobic	false
C7M	CG2	VAL- 51	3.57	0	Hydrophobic	false
C1'	SD	MET- 54	4.32	0	Hydrophobic	false
C9A	SD	MET- 54	3.67	0	Hydrophobic	false
O4'	OD2	ASP- 98	2.82	167.69	H-Bond (Ligand Donor)	false
O1P	OG1	THR- 100	2.53	162.81	H-Bond (Protein Donor)	false
C5B	CG	PHE- 102	3.94	0	Hydrophobic	false
C4B	CD2	PHE- 102	3.79	0	Hydrophobic	false
C5'	CD1	PHE- 102	3.88	0	Hydrophobic	false
O3'	NH1	ARG- 106	3.36	142.06	H-Bond (Protein Donor)	false
O4'	NH2	ARG- 106	3.18	142.31	H-Bond (Protein Donor)	false
O2'	NZ	LYS- 221	3.03	147.9	H-Bond (Protein Donor)	false
C8M	CZ	PHE- 222	3.92	0	Hydrophobic	false
C1'	CE1	PHE- 222	4.27	0	Hydrophobic	false
N6A	OE1	GLU- 331	3	149.19	H-Bond (Ligand Donor)	false
N7A	OH	TYR- 341	2.61	162.33	H-Bond (Protein Donor)	false
N6A	OH	TYR- 341	2.95	152.17	H-Bond (Ligand Donor)	false
C8M	CD1	TYR- 341	4.23	0	Hydrophobic	false
O2	O	HOH- 5040	2.75	154.54	H-Bond (Protein Donor)	false