scPDB - 2zbv entry

Protein Data Bank Entry:

PDB ID : 2zbv

Resolution :2.050 Å

Experimental Method : X-ray

Deposition Date : 2007-10-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uncharacterized protein
ID:	Q9WZC8_THEMA
AC:	Q9WZC8
Organism:	Thermotoga maritima
Reign:	Bacteria
TaxID:	243274
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	55 %
C	45 %

Ligand binding site composition:

B-Factor:	25.064
Number of residues:	33
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.648	317.250

% Hydrophobic	% Polar
59.57	40.43
According to VolSite

Ligand :

HET Code:	ADN
Formula:	C10H13N5O4
Molecular weight:	267.241 g/mol
DrugBank ID:	DB00640
Buried Surface Area:	82.95 %
Polar Surface area:	139.54 Å2

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

Mass center Coordinates

X	Y	Z
40.3826	47.6433	24.3194

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
O3'	OD1	ASP- 7	2.82	157.38	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 7	3.48	121.69	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 7	2.75	162.3	H-Bond (Ligand Donor)	false
C5'	CE2	TRP- 8	4.3	0	Hydrophobic	false
O3'	NE1	TRP- 8	3.29	136.76	H-Bond (Protein Donor)	false
C2'	CD1	PHE- 41	4.42	0	Hydrophobic	false
C4'	CB	ASP- 68	4.26	0	Hydrophobic	false
O3'	N	ASP- 68	2.84	172.09	H-Bond (Protein Donor)	false
C4'	CG1	VAL- 71	4.41	0	Hydrophobic	false
C1'	CG1	VAL- 71	4.35	0	Hydrophobic	false
O5'	O	THR- 125	2.66	128.4	H-Bond (Ligand Donor)	false
C5'	CD1	PHE- 126	4.34	0	Hydrophobic	false
C2'	CZ	PHE- 180	3.69	0	Hydrophobic	false
N7	ND2	ASN- 182	3.07	176.95	H-Bond (Protein Donor)	false
N6	OD1	ASN- 182	3.06	156.49	H-Bond (Ligand Donor)	false
C1'	CE2	PHE- 220	4.23	0	Hydrophobic	false
DuAr	DuAr	PHE- 220	3.69	0	Aromatic Face/Face	false
N6	O	VAL- 242	2.92	169.7	H-Bond (Ligand Donor)	false
N1	N	LEU- 244	2.88	167.22	H-Bond (Protein Donor)	false