scPDB - 3wb2 entry

Protein Data Bank Entry:

PDB ID : 3wb2

Resolution :2.440 Å

Experimental Method : X-ray

Deposition Date : 2013-05-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uncharacterized protein MJ0488
ID:	Y488_METJA
AC:	Q57912
Organism:	Methanocaldococcus jannaschii
Reign:	Archaea
TaxID:	243232
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	79 %
B	21 %

Ligand binding site composition:

B-Factor:	43.650
Number of residues:	40
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:	GDP
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.176	617.625

% Hydrophobic	% Polar
30.05	69.95
According to VolSite

Ligand :

HET Code:	YGP
Formula:	C17H20N6O9P
Molecular weight:	483.349 g/mol
DrugBank ID:	-
Buried Surface Area:	69.03 %
Polar Surface area:	232.48 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	5
Rings:	4
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
18.1238	-16.6682	11.551

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
OAD	NH2	ARG- 20	2.89	157.38	H-Bond (Protein Donor)	false
OAD	NE	ARG- 20	3.16	146.6	H-Bond (Protein Donor)	false
CAB	CG	ARG- 20	4.42	0	Hydrophobic	false
CAA	CB	ASP- 23	4.33	0	Hydrophobic	false
NAO	OD1	ASP- 23	2.81	172.62	H-Bond (Ligand Donor)	false
OAI	NZ	LYS- 50	3.44	125.98	H-Bond (Protein Donor)	false
OAF	NZ	LYS- 50	2.52	133.95	H-Bond (Protein Donor)	false
OAI	NZ	LYS- 50	3.44	0	Ionic (Protein Cationic)	false
OAF	NZ	LYS- 50	2.52	0	Ionic (Protein Cationic)	false
OAF	NZ	LYS- 86	3.75	0	Ionic (Protein Cationic)	false
N7	NH2	ARG- 102	3.42	166.16	H-Bond (Protein Donor)	false
OAI	CZ	ARG- 102	3.61	0	Ionic (Protein Cationic)	false
OAD	NH1	ARG- 104	2.79	161.64	H-Bond (Protein Donor)	false
CAB	CB	ARG- 104	4.38	0	Hydrophobic	false
O6	NE2	HIS- 135	2.85	121.32	H-Bond (Protein Donor)	false
N2	O	GLU- 137	2.8	140.38	H-Bond (Ligand Donor)	false
N1	O	GLU- 137	2.73	139.59	H-Bond (Ligand Donor)	false
C3'	CD1	ILE- 139	4.06	0	Hydrophobic	false
O2'	N7	GDP- 204	2.83	160.11	H-Bond (Ligand Donor)	false
O3'	O2A	GDP- 204	2.78	153.98	H-Bond (Ligand Donor)	false