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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

3wbz

2.390 Å

X-ray

2013-05-24

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:tRNA(His) guanylyltransferase {ECO:0000256|PIRNR:PIRNR028980}
ID:Q5AFK5_CANAL
AC:Q5AFK5
Organism:Candida albicans
Reign:Eukaryota
TaxID:237561
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
C94 %
D6 %


Ligand binding site composition:

B-Factor:39.655
Number of residues:33
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 4
Water Molecules: 0
Cofactors: ATP
Metals: MG MG MG

Cavity properties

LigandabilityVolume (Å3)
0.3152281.500

% Hydrophobic% Polar
30.4769.53
According to VolSite

Ligand :
3wbz_3 Structure
HET Code: ATP
Formula: C10H12N5O13P3
Molecular weight: 503.149 g/mol
DrugBank ID: DB00171
Buried Surface Area:54.47 %
Polar Surface area: 319.88 Å2
Number of
H-Bond Acceptors: 17
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
14.856452.2175-6.43916


Binding mode :
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Binding mode
BioSolveIT 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
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
O3GNGLY- 322.79176.55H-Bond
(Protein Donor)
O1BNPHE- 332.91157.78H-Bond
(Protein Donor)
C5'CBPHE- 333.970Hydrophobic
O2BNHIS- 343.05163.17H-Bond
(Protein Donor)
O2BND1HIS- 342.98120.94H-Bond
(Protein Donor)
C1'CBSER- 374.130Hydrophobic
N3NZLYS- 443.12168.29H-Bond
(Protein Donor)
N6OASP- 473.24164.28H-Bond
(Ligand Donor)
N1NASP- 472.74151.3H-Bond
(Protein Donor)
C5'CBASP- 764.450Hydrophobic
O2AMG MG- 4032.260Metal Acceptor
O2GMG MG- 4042.060Metal Acceptor
O1BMG MG- 4042.040Metal Acceptor
O2AMG MG- 4042.130Metal Acceptor