scPDB - 2x60 entry

Protein Data Bank Entry:

PDB ID : 2x60

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2010-02-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Mannose-1-phosphate guanylyltransferase
ID:	Q9X0C3_THEMA
AC:	Q9X0C3
Organism:	Thermotoga maritima
Reign:	Bacteria
TaxID:	243274
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	50.403
Number of residues:	39
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.330	985.500

% Hydrophobic	% Polar
31.51	68.49
According to VolSite

Ligand :

HET Code:	GTP
Formula:	C10H12N5O14P3
Molecular weight:	519.149 g/mol
DrugBank ID:	DB04137
Buried Surface Area:	72.83 %
Polar Surface area:	335.56 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
5.07181	-16.5641	-15.8907

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
C4'	CB	LEU- 7	4.21	0	Hydrophobic	false
C1'	CB	LEU- 7	3.65	0	Hydrophobic	false
O3'	O	LEU- 7	2.57	151.63	H-Bond (Ligand Donor)	false
N3	N	GLY- 9	2.86	137.87	H-Bond (Protein Donor)	false
O2'	N	GLY- 10	3.02	147.56	H-Bond (Protein Donor)	false
O3B	N	GLY- 12	3.07	120.95	H-Bond (Protein Donor)	false
O1B	N	GLY- 12	3.11	137.73	H-Bond (Protein Donor)	false
O1G	N	GLU- 13	3.25	146.17	H-Bond (Protein Donor)	false
O2G	NH2	ARG- 14	2.96	125.41	H-Bond (Protein Donor)	false
O3G	NH2	ARG- 14	3.44	131.33	H-Bond (Protein Donor)	false
O3G	NE	ARG- 14	2.76	176.5	H-Bond (Protein Donor)	false
O3G	N	ARG- 14	3.08	167.67	H-Bond (Protein Donor)	false
O2G	CZ	ARG- 14	3.57	0	Ionic (Protein Cationic)	false
O3G	CZ	ARG- 14	3.55	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 25	3.44	134	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 25	3.44	0	Ionic (Protein Cationic)	false
N2	O	VAL- 56	3.05	143.5	H-Bond (Ligand Donor)	false
N1	OE2	GLU- 80	3.44	148	H-Bond (Ligand Donor)	false
N1	OE1	GLU- 80	2.73	132.85	H-Bond (Ligand Donor)	false
N2	OE1	GLU- 80	2.75	132.75	H-Bond (Ligand Donor)	false
O6	N	LYS- 84	3.32	122.24	H-Bond (Protein Donor)	false
C1'	CG2	THR- 86	4.34	0	Hydrophobic	false
C5'	CG2	THR- 86	4.21	0	Hydrophobic	false
C4'	CB	PRO- 107	4.2	0	Hydrophobic	false
O3'	N	ALA- 108	3.18	154.28	H-Bond (Protein Donor)	false
O2G	MG	MG- 602	2.26	0	Metal Acceptor	false
O2B	MG	MG- 602	2.27	0	Metal Acceptor	false
O1A	MG	MG- 602	2.48	0	Metal Acceptor	false