scPDB - 3clt entry

Protein Data Bank Entry:

PDB ID : 3clt

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2008-03-20

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_METME
AC:	P53571
Organism:	Methylophilus methylotrophus
Reign:	Bacteria
TaxID:	17
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
C	16 %
D	84 %

Ligand binding site composition:

B-Factor:	15.933
Number of residues:	53
Including
Standard Amino Acids:	49
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.157	1265.625

% Hydrophobic	% Polar
42.40	57.60
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	70.95 %
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
72.0291	56.6945	-12.9078

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	CZ2	TRP- 38	3.72	0	Hydrophobic	false
C8M	CG1	VAL- 120	3.9	0	Hydrophobic	false
C8M	CG	GLN- 121	4.19	0	Hydrophobic	false
C7M	CG1	VAL- 145	4.17	0	Hydrophobic	false
C1'	CD1	LEU- 184	4.02	0	Hydrophobic	false
O1A	NE	ARG- 210	2.85	169.09	H-Bond (Protein Donor)	false
O2P	N	ARG- 210	2.88	163.9	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 210	3.63	0	Ionic (Protein Cationic)	false
C5B	CB	ARG- 210	4.03	0	Hydrophobic	false
O2P	OG	SER- 235	2.6	169.41	H-Bond (Protein Donor)	false
O2	N	GLU- 236	2.92	151.08	H-Bond (Protein Donor)	false
C1'	CB	GLU- 236	4.19	0	Hydrophobic	false
C5'	CG	PRO- 237	4.11	0	Hydrophobic	false
O4	NE2	GLN- 249	3.04	165.22	H-Bond (Protein Donor)	false
N3	O	VAL- 250	2.74	147.56	H-Bond (Ligand Donor)	false
C6	CB	GLN- 252	4.35	0	Hydrophobic	false
N5	N	SER- 253	3.32	158.32	H-Bond (Protein Donor)	false
C6	CB	SER- 253	3.98	0	Hydrophobic	false
O4	N	GLY- 254	3.08	143.3	H-Bond (Protein Donor)	false
O2A	OG	SER- 269	2.66	166.54	H-Bond (Protein Donor)	false
O5B	N	SER- 269	3.44	123.45	H-Bond (Protein Donor)	false
O1P	N	SER- 269	2.8	153.94	H-Bond (Protein Donor)	false
C3B	CB	SER- 269	4.18	0	Hydrophobic	false
O4'	OG	SER- 271	2.68	121.19	H-Bond (Protein Donor)	false
C2'	CB	SER- 271	3.79	0	Hydrophobic	false
C9A	CB	GLN- 273	3.32	0	Hydrophobic	false
C2'	CB	GLN- 273	4.5	0	Hydrophobic	false
C9	CG	GLN- 273	3.57	0	Hydrophobic	false
O3B	ND2	ASN- 288	2.95	163.1	H-Bond (Protein Donor)	false
O2B	OD1	ASN- 288	2.79	155.26	H-Bond (Ligand Donor)	false
N3A	N	THR- 289	3.32	162.19	H-Bond (Protein Donor)	false
N6A	OD2	ASP- 306	2.91	157.81	H-Bond (Ligand Donor)	false
N1A	N	ILE- 307	3.17	159.58	H-Bond (Protein Donor)	false