scPDB - 3g6w entry

Protein Data Bank Entry:

PDB ID : 3g6w

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2009-02-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uracil phosphoribosyltransferase
ID:	UPP_SULSO
AC:	Q980Q4
Organism:	Sulfolobus solfataricus
Reign:	Archaea
TaxID:	273057
EC Number:	2.4.2.9

Chains:

Chain Name:	Percentage of Residues within binding site
A	4 %
B	40 %
C	20 %
D	36 %

Ligand binding site composition:

B-Factor:	31.329
Number of residues:	25
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	3
Water Molecules:	0
Cofactors:	GTP GTP
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.560	1086.750

% Hydrophobic	% Polar
34.47	65.53
According to VolSite

Ligand :

HET Code:	GTP
Formula:	C10H12N5O14P3
Molecular weight:	519.149 g/mol
DrugBank ID:	DB04137
Buried Surface Area:	54.38 %
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
-9.20497	3.30975	6.78944

Binding mode :

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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
O3G	NZ	LYS- 30	2.6	152.24	H-Bond (Protein Donor)	false
O3G	NZ	LYS- 30	2.6	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 30	3.46	0	Ionic (Protein Cationic)	false
O2G	NH1	ARG- 34	2.97	121.84	H-Bond (Protein Donor)	false
O6	NH2	ARG- 34	2.87	139.98	H-Bond (Protein Donor)	false
O1G	NH1	ARG- 37	2.96	146.4	H-Bond (Protein Donor)	false
O3B	NH1	ARG- 37	3.2	141.16	H-Bond (Protein Donor)	false
O3B	NH2	ARG- 37	3.01	150.99	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 37	3.17	127.71	H-Bond (Protein Donor)	false
O1G	CZ	ARG- 37	3.9	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 91	2.83	171.04	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 91	3.42	143.56	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 91	2.83	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 91	3.42	0	Ionic (Protein Cationic)	false
C4'	CB	PRO- 94	3.6	0	Hydrophobic	false
C1'	CB	PRO- 94	3.99	0	Hydrophobic	false
C3'	CG	PRO- 94	4.24	0	Hydrophobic	false
O1B	MG	MG- 302	2.02	0	Metal Acceptor	false
O1A	MG	MG- 302	2.06	0	Metal Acceptor	false