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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:

3tif

1.800 Å

X-ray

2011-08-20

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Uncharacterized ABC transporter ATP-binding protein MJ0796
ID:Y796_METJA
AC:Q58206
Organism:Methanocaldococcus jannaschii
Reign:Archaea
TaxID:243232
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A69 %
B31 %


Ligand binding site composition:

B-Factor:42.191
Number of residues:37
Including
Standard Amino Acids: 35
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals: NA

Cavity properties

LigandabilityVolume (Å3)
0.602918.000

% Hydrophobic% Polar
31.6268.38
According to VolSite

Ligand :
3tif_1 Structure
HET Code: ADP
Formula: C10H12N5O10P2
Molecular weight: 424.177 g/mol
DrugBank ID: -
Buried Surface Area:67.42 %
Polar Surface area: 260.7 Å2
Number of
H-Bond Acceptors: 14
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 3
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 6

Mass center Coordinates

XYZ
35.27762.12526-15.4897


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
DuArDuArTYR- 113.510Aromatic Face/Face
C4'CBALA- 204.20Hydrophobic
O3BNGLY- 412.74158.92H-Bond
(Protein Donor)
O2BNGLY- 432.9138.46H-Bond
(Protein Donor)
O3ANGLY- 433.25141.27H-Bond
(Protein Donor)
O2BNLYS- 442.82163H-Bond
(Protein Donor)
O2BNZLYS- 442.82163.12H-Bond
(Protein Donor)
O2BNZLYS- 442.820Ionic
(Protein Cationic)
O3BNZLYS- 443.60Ionic
(Protein Cationic)
O1BNSER- 452.8164.58H-Bond
(Protein Donor)
O1ANTHR- 463.21144.39H-Bond
(Protein Donor)
O3'NE2GLN- 11503.09152.49H-Bond
(Protein Donor)
O2'OE1GLN- 11502.8165.2H-Bond
(Ligand Donor)