CoeSFMs: Coenzymes Binding Structural & Functional Motifs - v. β November 2015.
© University Dr Tahar Moulay, Saida.


Project realized by:Brahimi Mohamed (in his project of MSc of Biology, 2014-2015)

Proposed & supervised by: Dr. Abdelkrim Rachedi, e-mail: rachedi@bioinformaticstools.org

Coenzymes Binding Structural & Functional Motifs
- CoeSFMs -
Find CoeSFMs by Ligands:
UQ   UQ2   NAD   COA   CAO   COD   882   NDP   NAP   ATP   FAD   FDA   CNC   B12   TPP   HTL   TMV   PXP   PLP   HEM   
Find CoeSFMs by PDB entries:
1DLV   1DQ8   1QAX   1R31   1T3Z   1YQZ   2Q1L   2VJK   3RBA   1YQ4   1ZOY   3CWB   3H1H   3L73   1OQC   2F5V   2F6C   2I0Z   3MBG   3R7C   3TK0   3U2M   3U5S   4LDK   1AHH   1EMD   1FK8   1SUW   1TOX   1XHL   1Z0U   1Z0Z   1ZBQ   2GDZ   2ZIT   3B78   3B82   3I9K   3UQ8   3ZWM   1B14   1N5D   1XKQ   4PVD   1IPE   1PGO   1FRB   1MAR   4ZQB   4G62   4BRH   3AHD   3M34   3M6L   3M7I   3EKI   2XIJ   2XIQ   3HWX   3LGX   3QXC   4CO3   4CO4   4TSF   1N2Z   4TT3   4Z1M   1NTZ   1YQ3   1N4A   3O0O   1HO4   3O6D   1NRG   1JNW   3HY8   1G76   3GAH   5A65   2AQ6   4D79   4QNR   4GI2   4EU9   4IV6   4HNH   4K6F   4Z0P   4WDT   4XYE   1RCQ   1VP4   4ATQ   1RFU   4RAS   4WH3   3WV8   4XW5   2VIG   2WBI   3NF4   3MPI   3OWA   4HR3   3DFR   8DFR   
Finding CoeSFMs for the coenzyme/vitamin 'ATP' ...
Ligand: IDFull NameFormula Chemistry
ATPADENOSINE-5'-TRIPHOSPHATEC10 H16 N5 O13 P3ATP
There are 27 CoeSFMs:
Nbr of Motifs
per PDB entry		 PDB EntryTitleDetermination MethodResolutionR-Factor
43LGXStructure of probable D-alanine-poly(phosphoribitol) ligase subunit-1 from Streptococcus pyogenes with ATPX-RAY2.600.221
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)		Show Details
1 / A   > Structure: SLHLLLLSLHLSSLL +2w
  > Sequence: TSFDGEENAYGPTITDYRNK 		ATP
/(600)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
2 / B   > Structure: SLHLLLLSLHLSSLL +1w
  > Sequence: TSFDGEENAYGPTEIDYRNK 		ATP
/(600)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
3 / C   > Structure: SLHSLLLSLHLSSLL
  > Sequence: TSFDGEENAYGPTITDYRNK 		ATP
/(600)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
4 / D   > Structure: LLSLLLSLHLSSLL +1w
  > Sequence: SFDGEENAYGPTEIDYRNK 		ATP
/(600)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry		 PDB EntryTitleDetermination MethodResolutionR-Factor
13QXCCrystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with ATPX-RAY1.340.140
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)		Show Details
1 / A   > Structure: LLLHLHSLLL +14w
  > Sequence: TNAGKTTKDENKQ 		ATP
/(221)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry		 PDB EntryTitleDetermination MethodResolutionR-Factor
24CO3Structure of PII signaling protein GlnZ from Azospirillum brasilense in complex with adenosine triphosphateX-RAY1.050.171
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)		Show Details
1 / A   > Structure: LLLSSLL +4w
  > Sequence: IGLTEVARR 		ATP
/(113)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
2 / B   > Structure: SLLLSSLLL +7w
  > Sequence: LIGLTEVAVRRT 		ATP
/(113)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry		 PDB EntryTitleDetermination MethodResolutionR-Factor
24CO4Structure of PII signaling protein GlnZ from Azospirillum brasilense in complex with adenosine triphosphateX-RAY1.500.168
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)		Show Details
1 / A   > Structure: SSSSLLLLS +8w
  > Sequence: IGFKIGDGKF 		ATP
/(120)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
2 / B   > Structure: SSSLLLLS +9w
  > Sequence: IGFKIGDGKF 		ATP
/(120)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry		 PDB EntryTitleDetermination MethodResolutionR-Factor
34TSFThe Pathway of Binding of the Intrinsically Disordered Mitochondrial Inhibitor Protein to F1-ATPaseX-RAY3.200.236
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)		Show Details
1 / A   > Structure: LLLLHHLLLL +2w
  > Sequence: DRQTGKTSFRPQQ 		ATP
/(600)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
2 / B   > Structure: LLLHHLLL +2w
  > Sequence: DQTGKTSFRQQ 		ATP
/(600)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
3 / C   > Structure: LLLHHLLLL +2w
  > Sequence: DQTGKTSFRPQQ 		ATP
/(600)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry		 PDB EntryTitleDetermination MethodResolutionR-Factor
34TT3The Pathway of Binding of the Intrinsically Disordered Mitochondrial Inhibitor Protein to F1-ATPaseX-RAY3.210.244
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)		Show Details
1 / A   > Structure: LLLHSHLLLL +2w
  > Sequence: DQTGKTSEFRPQQ 		ATP
/(601)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
2 / B   > Structure: LLLHHLLLL +2w
  > Sequence: DQTGKTSFRQGQ 		ATP
/(601)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
3 / C   > Structure: LLLHHLLLL +2w
  > Sequence: QTGKTSFRPQQ 		ATP
/(600)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry		 PDB EntryTitleDetermination MethodResolutionR-Factor
34Z1MBovine F1-ATPase inhibited by three copies of the inhibitor protein IF1 crystallised in the presence of thiophosphateX-RAY3.300.240
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)		Show Details
1 / A   > Structure: LLLLHSHLLLL +3w
  > Sequence: DRQTGKTSEFRPQQ 		ATP
/(601)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
2 / B   > Structure: LLLLHSHLLL +2w
  > Sequence: DRQTGKTSEFRQQ 		ATP
/(601)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
3 / C   > Structure: LLLHHLLLL +3w
  > Sequence: DQTGKTSFRQGQ 		ATP
/(601)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry		 PDB EntryTitleDetermination MethodResolutionR-Factor
13GAHSTRUCTURE OF A F112H VARIANT PDUO-TYPE ATP:CORRINOID ADENOSYLTRANSFERASE FROM LACTOBACILLUS REUTERI COMPLEXED WI COBALAMIN AND ATPX-RAY1.170.161
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)		Show Details
1 / A   > Structure: LLLLLLSLH +5w
  > Sequence: IYTKNGQTRKVYG 		ATP
/(999)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry		 PDB EntryTitleDetermination MethodResolutionR-Factor
44D79CRYSTAL STRUCTURE OF E. COLI TRNA N6-THREONYLCARBAMOYLADENOS DEHYDRATASE, TCDA, IN COMPLEX WITH ATPX-ray1.770.144
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)		Show Details
1 / A   > Structure: SLLLLSLLHLLHLLLLLH +5w
  > Sequence: VGIGGIDDNRQKFVAIDSP 		ATP
/(401)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
2 / B   > Structure: SLLLSLLHLHLLLLLLH +5w
  > Sequence: VGGGIDDNRQKDFVAIDP 		ATP
/(401)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
3 / C   > Structure: SLLLLSLLHLLHLLLLLLH +5w
  > Sequence: VGIGGIDDNRQKDFVAIDSP 		ATP
/(401)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
4 / D   > Structure: SLLLLSLHLHLLLLLH +5w
  > Sequence: VGIGGIDDNRQKFVAIDSP 		ATP
/(401)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry		 PDB EntryTitleDetermination MethodResolutionR-Factor
14QNRCRYSTAL STRUCTURE OF PSPF(1-265) E108Q MUTANT BOUND TO ATPX-ray1.540.149
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)		Show Details
1 / A   > Structure: LLLHLLLLHSHH +9w
  > Sequence: NLLFERGTGKELDMFIR 		ATP
/(301)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry		 PDB EntryTitleDetermination MethodResolutionR-Factor
14WH3N-acetylhexosamine 1-kinase in complex with ATPX-ray1.800.191
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)		Show Details
1 / A   > Structure: LLLLLLSSLSLLLLLL +11w
  > Sequence: GDGHINTIQLYKFINIDD 		ATP
/(401)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry		 PDB EntryTitleDetermination MethodResolutionR-Factor
23WV8ATP-bound HcgE from Methanothermobacter marburgensisX-ray1.800.195
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)		Show Details
1 / A   > Structure: SHSLLHLLLLLLLH +9w
  > Sequence: VGRLIDQKYIEIAVVL 		ATP
/(301)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
2 / B   > Structure: SLHSLLHLLLLLLLH +5w
  > Sequence: VGGRLIDQKYIEIAVVL 		ATP
/(301)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]