scPDB - 3mj4 entry

Protein Data Bank Entry:

PDB ID : 3mj4

Resolution :2.650 Å

Experimental Method : X-ray

Deposition Date : 2010-04-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	UDP-galactopyranose mutase
ID:	Q9RYF1_DEIRA
AC:	Q9RYF1
Organism:	Deinococcus radiodurans
Reign:	Bacteria
TaxID:	243230
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	53.987
Number of residues:	43
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.952	1137.375

% Hydrophobic	% Polar
44.51	55.49
According to VolSite

Ligand :

HET Code:	URM
Formula:	C16H24N2O16P2
Molecular weight:	562.313 g/mol
DrugBank ID:	-
Buried Surface Area:	69.22 %
Polar Surface area:	307.59 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	7
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
77.0762	-71.3902	39.4127

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
N15	O	PHE- 175	2.91	145.06	H-Bond (Ligand Donor)	false
C1	CD1	PHE- 176	3.94	0	Hydrophobic	false
C3	CE2	TYR- 179	4.28	0	Hydrophobic	false
C2	CD2	TYR- 179	3.78	0	Hydrophobic	false
O21	OG1	THR- 180	2.74	162.43	H-Bond (Ligand Donor)	false
O7	NE1	TRP- 184	2.76	144.22	H-Bond (Protein Donor)	false
O21	NE1	TRP- 184	3.31	135.49	H-Bond (Protein Donor)	false
C4	CG1	VAL- 195	3.9	0	Hydrophobic	false
C1	CG2	THR- 196	3.91	0	Hydrophobic	false
C5	CB	ARG- 198	4.36	0	Hydrophobic	false
C1	CG2	VAL- 199	4.43	0	Hydrophobic	false
C5	CG2	VAL- 199	3.91	0	Hydrophobic	false
O11	OH	TYR- 209	3	156.17	H-Bond (Protein Donor)	false
O12	OH	TYR- 209	3.03	129.99	H-Bond (Protein Donor)	false
C46	CE2	TYR- 209	3.96	0	Hydrophobic	false
C46	CE2	PHE- 210	3.68	0	Hydrophobic	false
O20	ND2	ASN- 296	3.25	139.27	H-Bond (Protein Donor)	false
C40	CD	ARG- 305	4.29	0	Hydrophobic	false
C39	C6	FAD- 450	4.06	0	Hydrophobic	false
O42	O4	FAD- 450	2.79	125.88	H-Bond (Ligand Donor)	false
O43	N5	FAD- 450	2.89	170.97	H-Bond (Ligand Donor)	false
O24	O	HOH- 586	3.12	165.52	H-Bond (Protein Donor)	false