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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:

3nmu

2.730 Å

X-ray

2010-06-22

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
ID:FLPA_PYRFU
AC:Q8U4M2
Organism:Pyrococcus furiosus
Reign:Archaea
TaxID:186497
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A15 %
G3 %
F82 %


Ligand binding site composition:

B-Factor:68.630
Number of residues:33
Including
Standard Amino Acids: 33
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.8381620.000

% Hydrophobic% Polar
31.8868.13
According to VolSite

Ligand :
3nmu_1 Structure
HET Code: SAM
Formula: C15H23N6O5S
Molecular weight: 399.445 g/mol
DrugBank ID: DB00118
Buried Surface Area:57.74 %
Polar Surface area: 189.77 Å2
Number of
H-Bond Acceptors: 9
H-Bond Donors: 4
Rings: 3
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 2
Rule of Five Violation: 1
Rotatable Bonds: 7

Mass center Coordinates

XYZ
58.26232.96812-20.9852


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
ONZLYS- 573.45133.96H-Bond
(Protein Donor)
CECBALA- 833.550Hydrophobic
C4'CBALA- 834.330Hydrophobic
O3'OE1GLU- 1053.19167.06H-Bond
(Ligand Donor)
N3NPHE- 1063.27142.02H-Bond
(Protein Donor)
N6OD1ASP- 1303.42138.81H-Bond
(Ligand Donor)
N1NALA- 1312.81157.81H-Bond
(Protein Donor)
C3'CBGLU- 3523.930Hydrophobic
C2'CBTYR- 3534.310Hydrophobic
O2'NTYR- 3533.25149.11H-Bond
(Protein Donor)