scPDB - 3tlc entry

Protein Data Bank Entry:

PDB ID : 3tlc

Resolution :1.300 Å

Experimental Method : X-ray

Deposition Date : 2011-08-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Microcin C7 self-immunity protein MccF
ID:	MCCF_ECOLX
AC:	Q47511
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	562
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	3 %
B	97 %

Ligand binding site composition:

B-Factor:	8.043
Number of residues:	40
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.170	448.875

% Hydrophobic	% Polar
36.09	63.91
According to VolSite

Ligand :

HET Code:	7MD
Formula:	C17H28N8O9P
Molecular weight:	519.426 g/mol
DrugBank ID:	-
Buried Surface Area:	50.5 %
Polar Surface area:	289.16 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	3
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
13.2564	0.538	48.9575

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
C33	CB	ALA- 26	4.06	0	Hydrophobic	false
C33	CD1	ILE- 90	4.45	0	Hydrophobic	false
C5'	CG1	ILE- 90	4.44	0	Hydrophobic	false
O1P	N	GLY- 91	3	132.22	H-Bond (Protein Donor)	false
O	N	GLY- 92	2.81	163.91	H-Bond (Protein Donor)	false
C5'	CZ	TYR- 117	4.33	0	Hydrophobic	false
O	N	ASP- 119	3.09	146.83	H-Bond (Protein Donor)	false
CB	CB	ASP- 119	4.28	0	Hydrophobic	false
C4'	CB	PRO- 143	3.96	0	Hydrophobic	false
C1'	CZ3	TRP- 186	3.49	0	Hydrophobic	false
C4'	CH2	TRP- 186	4.38	0	Hydrophobic	false
OD2	ND2	ASN- 220	2.89	166.55	H-Bond (Protein Donor)	false
O2'	NE	ARG- 246	2.96	148.83	H-Bond (Protein Donor)	false
O2'	NH2	ARG- 246	2.98	145.15	H-Bond (Protein Donor)	false
OD1	NZ	LYS- 247	3.15	138.81	H-Bond (Protein Donor)	false
OD1	NZ	LYS- 247	3.15	0	Ionic (Protein Cationic)	false
O2'	OE1	GLU- 277	3.34	149.06	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 277	2.78	143.46	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 277	2.71	161.36	H-Bond (Ligand Donor)	false
OD1	O	HOH- 354	2.8	148.85	H-Bond (Protein Donor)	false
N	O	HOH- 357	2.95	125.46	H-Bond (Ligand Donor)	false