scPDB - 3awi entry

Protein Data Bank Entry:

PDB ID : 3awi

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 2011-03-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC
ID:	MNMC_ECOLI
AC:	P77182
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	1.5

Chains:

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

Ligand binding site composition:

B-Factor:	88.104
Number of residues:	66
Including
Standard Amino Acids:	66
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.825	1758.375

% Hydrophobic	% Polar
39.54	60.46
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	72.41 %
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
20.3992	162.931	72.0386

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
C5'	CG2	ILE- 274	4.23	0	Hydrophobic	false
O1P	N	ALA- 275	3.02	149.84	H-Bond (Protein Donor)	false
N3A	N	ALA- 295	2.88	129.75	H-Bond (Protein Donor)	false
O1A	N	ALA- 303	2.92	156.05	H-Bond (Protein Donor)	false
C8M	CB	ALA- 303	3.95	0	Hydrophobic	false
C9	CB	ALA- 303	4.13	0	Hydrophobic	false
C3'	CB	ALA- 303	3.65	0	Hydrophobic	false
O2A	OG	SER- 304	2.57	160.72	H-Bond (Protein Donor)	false
O4'	OG	SER- 304	2.98	137	H-Bond (Ligand Donor)	false
N3	O	ALA- 310	3.13	160.62	H-Bond (Ligand Donor)	false
N6A	O	LEU- 432	3.14	158.18	H-Bond (Ligand Donor)	false
N1A	N	LEU- 432	2.82	159.2	H-Bond (Protein Donor)	false
C1B	CB	ASN- 461	4.2	0	Hydrophobic	false
C7M	CG2	VAL- 483	3.85	0	Hydrophobic	false
C8M	CB	ARG- 567	4.42	0	Hydrophobic	false
C3'	CB	ARG- 567	4.36	0	Hydrophobic	false
C8	CD	ARG- 567	4.37	0	Hydrophobic	false
C3'	CB	LEU- 615	4.49	0	Hydrophobic	false
C5'	CD1	LEU- 615	3.5	0	Hydrophobic	false
O2'	N	GLY- 619	2.78	126.89	H-Bond (Protein Donor)	false
O2	N	LEU- 620	2.69	141.41	H-Bond (Protein Donor)	false
C1'	CD1	LEU- 620	4.48	0	Hydrophobic	false