scPDB - 2b56 entry

Protein Data Bank Entry:

PDB ID : 2b56

Resolution :1.970 Å

Experimental Method : X-ray

Deposition Date : 2005-09-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	RNA editing complex protein MP57
ID:	Q86MV5_9TRYP
AC:	Q86MV5
Organism:	Trypanosoma brucei
Reign:	Eukaryota
TaxID:	5691
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	27.867
Number of residues:	42
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	2
Water Molecules:	7
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.286	823.500

% Hydrophobic	% Polar
29.10	70.90
According to VolSite

Ligand :

HET Code:	UTP
Formula:	C9H11N2O15P3
Molecular weight:	480.109 g/mol
DrugBank ID:	DB04005
Buried Surface Area:	51.72 %
Polar Surface area:	299.67 Å2

Number of
H-Bond Acceptors:	15
H-Bond Donors:	3
Rings:	2
Aromatic rings:	0
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
10.4204	36.8924	14.5952

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
C4'	SG	CYS- 83	4.39	0	Hydrophobic	false
O1B	N	SER- 85	3.2	154.79	H-Bond (Protein Donor)	false
O2G	OG	SER- 96	2.77	159.74	H-Bond (Protein Donor)	false
C5'	CB	ASP- 99	4.06	0	Hydrophobic	false
O2'	OD1	ASN- 277	2.58	166.13	H-Bond (Ligand Donor)	false
O2	ND2	ASN- 277	2.89	142.73	H-Bond (Protein Donor)	false
O3'	OG	SER- 278	3.23	139.43	H-Bond (Ligand Donor)	false
O2G	NZ	LYS- 300	2.53	165.26	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 300	2.53	0	Ionic (Protein Cationic)	false
O1G	NZ	LYS- 304	2.9	155.5	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 304	3.39	132.18	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 304	2.9	0	Ionic (Protein Cationic)	false
O2G	NZ	LYS- 304	3.39	0	Ionic (Protein Cationic)	false
O1G	OG	SER- 318	3.21	173.18	H-Bond (Protein Donor)	false
C2'	CD1	TYR- 319	3.98	0	Hydrophobic	false
C3'	CB	TYR- 319	4.14	0	Hydrophobic	false
O1A	MG	MG- 488	2.48	0	Metal Acceptor	false
O1B	MG	MG- 488	1.92	0	Metal Acceptor	false
O3G	MG	MG- 488	2.11	0	Metal Acceptor	false
N3	O	HOH- 633	2.78	177.29	H-Bond (Ligand Donor)	false
O4	O	HOH- 759	2.59	179.93	H-Bond (Protein Donor)	false
O2B	O	HOH- 814	2.9	169.12	H-Bond (Protein Donor)	false