scPDB - 1xzq entry

Protein Data Bank Entry:

PDB ID : 1xzq

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2004-11-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	tRNA modification GTPase MnmE
ID:	MNME_THEMA
AC:	Q9WYA4
Organism:	Thermotoga maritima
Reign:	Bacteria
TaxID:	243274
EC Number:	3.6.5

Chains:

Chain Name:	Percentage of Residues within binding site
A	57 %
B	43 %

Ligand binding site composition:

B-Factor:	70.829
Number of residues:	30
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.925	725.625

% Hydrophobic	% Polar
51.63	48.37
According to VolSite

Ligand :

HET Code:	FON
Formula:	C20H21N7O7
Molecular weight:	471.423 g/mol
DrugBank ID:	DB03256
Buried Surface Area:	56.14 %
Polar Surface area:	221.2 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	5
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
71.3931	50.8139	-7.55612

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
C4A	CG1	ILE- 16	4.28	0	Hydrophobic	false
C9	CG	GLU- 59	4.31	0	Hydrophobic	false
N10	OE1	GLU- 59	3.39	160.68	H-Bond (Ligand Donor)	false
C4A	CG2	VAL- 61	4.13	0	Hydrophobic	false
C6	CG2	VAL- 61	3.94	0	Hydrophobic	false
C15	CG2	VAL- 61	4.11	0	Hydrophobic	false
CG	CG	LYS- 69	4.33	0	Hydrophobic	false
OE1	NZ	LYS- 69	3.31	130.05	H-Bond (Protein Donor)	false
OE1	NZ	LYS- 69	3.31	0	Ionic (Protein Cationic)	false
CP1	CD1	TYR- 71	3.46	0	Hydrophobic	false
C16	CB	TYR- 71	4.2	0	Hydrophobic	false
N3	OE1	GLU- 78	2.75	126.47	H-Bond (Ligand Donor)	false
N8	O	MET- 80	3.5	139.99	H-Bond (Ligand Donor)	false
O1	NZ	LYS- 117	3.68	0	Ionic (Protein Cationic)	false
O2	NZ	LYS- 117	2.65	0	Ionic (Protein Cationic)	false
O2	NZ	LYS- 117	2.65	158.62	H-Bond (Protein Donor)	false