scPDB - 1efp entry

Protein Data Bank Entry:

PDB ID : 1efp

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 1998-12-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Electron transfer flavoprotein subunit alpha
ID:	ETFA_PARDE
AC:	P38974
Organism:	Paracoccus denitrificans
Reign:	Bacteria
TaxID:	266
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
C	85 %
D	15 %

Ligand binding site composition:

B-Factor:	18.377
Number of residues:	46
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.562	627.750

% Hydrophobic	% Polar
49.46	50.54
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	66.59 %
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
31.9102	1.49655	96.296

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
C8M	CD2	TYR- 13	3.41	0	Hydrophobic	false
C7M	CB	PRO- 37	4.05	0	Hydrophobic	false
C8M	CB	PRO- 37	4.33	0	Hydrophobic	false
C7M	CE2	PHE- 38	3.97	0	Hydrophobic	false
C7M	CG2	ILE- 124	3.87	0	Hydrophobic	false
C7M	CD1	LEU- 182	4.48	0	Hydrophobic	false
C6	CD2	LEU- 182	3.79	0	Hydrophobic	false
O2A	NH2	ARG- 201	3.01	152.27	H-Bond (Protein Donor)	false
O2A	NE	ARG- 201	3.29	140.33	H-Bond (Protein Donor)	false
O2P	N	ARG- 201	2.99	133.58	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 201	3.58	0	Ionic (Protein Cationic)	false
C5B	CB	ARG- 201	4.23	0	Hydrophobic	false
O2P	OG	SER- 226	2.61	161.35	H-Bond (Protein Donor)	false
O2	N	ARG- 227	3.27	146.13	H-Bond (Protein Donor)	false
C1'	CB	ARG- 227	3.64	0	Hydrophobic	false
C4'	CB	ARG- 227	4.46	0	Hydrophobic	false
C9A	CD	ARG- 227	4.16	0	Hydrophobic	false
C5'	CB	ALA- 228	4.35	0	Hydrophobic	false
N3	O	VAL- 241	2.94	168.62	H-Bond (Ligand Donor)	false
O4	N	THR- 244	2.96	161.43	H-Bond (Protein Donor)	false
N5	OG1	THR- 244	2.78	166.71	H-Bond (Protein Donor)	false
C6	CB	THR- 244	4.36	0	Hydrophobic	false
O1A	OG	SER- 259	3.01	160.2	H-Bond (Protein Donor)	false
O1P	N	SER- 259	3.11	155.59	H-Bond (Protein Donor)	false
C3B	CB	SER- 259	4.34	0	Hydrophobic	false
C3'	CB	ALA- 261	3.62	0	Hydrophobic	false
C9A	CB	GLN- 263	3.58	0	Hydrophobic	false
C2'	CB	GLN- 263	4.06	0	Hydrophobic	false
C9	CG	GLN- 263	3.65	0	Hydrophobic	false
O2'	OE1	GLN- 263	2.69	143.75	H-Bond (Ligand Donor)	false
O3B	ND2	ASN- 278	2.77	150.86	H-Bond (Protein Donor)	false
O2B	OD1	ASN- 278	2.91	158.28	H-Bond (Ligand Donor)	false
N3A	N	LYS- 279	2.97	135.02	H-Bond (Protein Donor)	false
N6A	OD1	ASP- 296	3.13	162.12	H-Bond (Ligand Donor)	false
N1A	N	LEU- 297	2.93	172.83	H-Bond (Protein Donor)	false