scPDB - 4f9f entry

Protein Data Bank Entry:

PDB ID : 4f9f

Resolution :2.810 Å

Experimental Method : X-ray

Deposition Date : 2012-05-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative glycosyltransferase
ID:	Q15JG1_STRHY
AC:	Q15JG1
Organism:	Streptomyces hygroscopicus subsp. limoneus
Reign:	Bacteria
TaxID:	264445
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	64.163
Number of residues:	37
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.850	1299.375

% Hydrophobic	% Polar
35.58	64.42
According to VolSite

Ligand :

HET Code:	GDP
Formula:	C10H12N5O11P2
Molecular weight:	440.177 g/mol
DrugBank ID:	DB04315
Buried Surface Area:	59.69 %
Polar Surface area:	276.39 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-56.4754	-39.8965	14.7124

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
N2	O	PRO- 32	2.81	154.27	H-Bond (Ligand Donor)	false
N3	O	PRO- 32	3.18	135.77	H-Bond (Ligand Donor)	false
O1B	NE	ARG- 290	3.17	134.58	H-Bond (Protein Donor)	false
O1B	NH2	ARG- 290	2.85	144.71	H-Bond (Protein Donor)	false
O3B	NE	ARG- 290	2.99	140.24	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 290	3.41	0	Ionic (Protein Cationic)	false
O1B	NZ	LYS- 295	3.15	0	Ionic (Protein Cationic)	false
O3A	NZ	LYS- 295	3.21	158.71	H-Bond (Protein Donor)	false
N2	OD1	ASN- 361	2.72	141.77	H-Bond (Ligand Donor)	false
O6	N	ASP- 362	3.36	123.98	H-Bond (Protein Donor)	false
C1'	CG2	VAL- 363	3.72	0	Hydrophobic	false
N7	OG1	THR- 366	3.12	146.07	H-Bond (Protein Donor)	false
O1A	N	LEU- 387	3.09	168.13	H-Bond (Protein Donor)	false
O2A	N	LEU- 387	3.15	123.08	H-Bond (Protein Donor)	false
O2A	N	SER- 388	3.02	158.9	H-Bond (Protein Donor)	false
O2A	OG	SER- 388	3.01	154.81	H-Bond (Protein Donor)	false
O3'	OE1	GLU- 391	2.59	169.5	H-Bond (Ligand Donor)	false
O2'	OE1	GLU- 391	2.98	155.2	H-Bond (Ligand Donor)	false