scPDB - 3amf entry

Protein Data Bank Entry:

PDB ID : 3amf

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2010-08-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	FMN-binding protein
ID:	FMNB_DESVM
AC:	Q46604
Organism:	Desulfovibrio vulgaris
Reign:	Bacteria
TaxID:	883
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	62 %
B	38 %

Ligand binding site composition:

B-Factor:	10.047
Number of residues:	34
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.760	489.375

% Hydrophobic	% Polar
44.14	55.86
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	70.82 %
Polar Surface area:	217.05 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-6.71977	-1.11287	-22.0548

Binding mode :

What is Poseview ?

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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
C7M	CG2	VAL- 15	3.93	0	Hydrophobic	false
O1P	NE2	HIS- 27	2.74	163.95	H-Bond (Protein Donor)	false
O3P	NE2	HIS- 27	3.44	124.41	H-Bond (Protein Donor)	false
C2'	CB	VAL- 29	4.13	0	Hydrophobic	false
C3'	CG1	VAL- 29	3.97	0	Hydrophobic	false
O2'	N	ASN- 30	2.83	153.65	H-Bond (Protein Donor)	false
C8	CB	ASN- 30	3.51	0	Hydrophobic	false
O4	OG1	THR- 31	2.77	153.49	H-Bond (Protein Donor)	false
C7M	CH2	TRP- 32	3.43	0	Hydrophobic	false
N3	O	PRO- 47	2.98	161.48	H-Bond (Ligand Donor)	false
O2	N	GLY- 49	2.76	153.03	H-Bond (Protein Donor)	false
O2	N	GLY- 50	3.01	147.27	H-Bond (Protein Donor)	false
O4'	N	MET- 51	2.81	149.1	H-Bond (Protein Donor)	false
O5'	N	MET- 51	3.09	120.79	H-Bond (Protein Donor)	false
O2P	N	HIS- 52	2.96	120.02	H-Bond (Protein Donor)	false
O2P	N	LYS- 53	3.04	171.94	H-Bond (Protein Donor)	false
O3P	N	THR- 54	2.83	154.92	H-Bond (Protein Donor)	false
O3P	OG1	THR- 54	2.74	156.21	H-Bond (Protein Donor)	false
C7	CD2	LEU- 122	3.95	0	Hydrophobic	false
C8	CB	LEU- 122	4.08	0	Hydrophobic	false