scPDB - 4idg entry

Protein Data Bank Entry:

PDB ID : 4idg

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2012-12-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative UDP-glucose 4-epimerase
ID:	A9CL58_AGRFC
AC:	A9CL58
Organism:	Agrobacterium fabrum )
Reign:	Bacteria
TaxID:	176299
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	18.302
Number of residues:	41
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.976	1437.750

% Hydrophobic	% Polar
40.85	59.15
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	67.39 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
2.397	5.26075	39.6939

Binding mode :

What is Poseview ?

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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
O1A	N	ARG- 10	2.93	177.09	H-Bond (Protein Donor)	false
O1N	NH1	ARG- 10	2.78	137.37	H-Bond (Protein Donor)	false
O1N	CZ	ARG- 10	3.98	0	Ionic (Protein Cationic)	false
O2N	N	VAL- 11	2.84	176.05	H-Bond (Protein Donor)	false
C5D	CB	VAL- 11	4.27	0	Hydrophobic	false
O3B	OD1	ASP- 30	3.4	127.34	H-Bond (Ligand Donor)	false
O3B	OD2	ASP- 30	2.6	163.44	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 30	2.6	158.7	H-Bond (Ligand Donor)	false
O3B	NH1	ARG- 32	2.99	141.69	H-Bond (Protein Donor)	false
N6A	OG	SER- 44	3.14	147.27	H-Bond (Ligand Donor)	false
N1A	N	LEU- 45	2.95	154.72	H-Bond (Protein Donor)	false
C5D	CB	LEU- 64	4.23	0	Hydrophobic	false
O4B	N	ALA- 66	3.35	152.14	H-Bond (Protein Donor)	false
C3D	CB	ALA- 66	4.09	0	Hydrophobic	false
C3N	CE	MET- 68	4.28	0	Hydrophobic	false
C4D	CB	ALA- 104	4.12	0	Hydrophobic	false
C5N	CB	SER- 106	3.72	0	Hydrophobic	false
O2D	OH	TYR- 132	2.55	160.3	H-Bond (Protein Donor)	false
O3D	NZ	LYS- 136	2.99	169.03	H-Bond (Protein Donor)	false
C4D	CE2	PHE- 159	4.06	0	Hydrophobic	false
C5N	CB	PHE- 159	4.03	0	Hydrophobic	false
O7N	N	THR- 162	2.79	156.26	H-Bond (Protein Donor)	false
O5B	O	HOH- 510	3.5	162.33	H-Bond (Protein Donor)	false