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 'FAD' ...
Ligand: IDFull NameFormula Chemistry
FADFLAVIN-ADENINE DINUCLEOTIDEC27 H33 N9 O15 P2FAD
There are 43 CoeSFMs:
Nbr of Motifs
per PDB entry
PDB EntryTitleDetermination MethodResolutionR-Factor
21YQZStructure of Coenzyme A-Disulfide Reductase from Staphylococcus aureus refinedX-RAY1.540.180
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)
Show Details
1 / A   > Structure: SLLLHSLLLHHSLLLLLHLHLLLH +13w
  > Sequence: VGVAGFEKDFNCPHEVSPGLRYVNFGDPLAA
FAD
/(439)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
2 / B   > Structure: SLLLHSLLLLHHSLLLLLHLHLLLH +15w
  > Sequence: VGVAGFEKDFNCPHEVSPGLRYNFGDPLAA
FAD
/(440)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry
PDB EntryTitleDetermination MethodResolutionR-Factor
11YQ4Avian respiratory complex ii with 3-nitropropionate and ubiquinoneX-RAY2.330.202
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)
Show Details
1 / A   > Structure: LLHSLLHLLLSLLLLLHLSLLLLH +10w
  > Sequence: GAGGAVTKLSHTAAQGGYFAATGTSDLHYGERANSLL
FAD
/(1001)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry
PDB EntryTitleDetermination MethodResolutionR-Factor
11ZOYCrystal Structure of Mitochondrial Respiratory Complex II from porcine heartX-RAY2.400.232
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)
Show Details
1 / A   > Structure: SLLHSLLHLLLSLLLLLHLSLLLLH +14w
  > Sequence: VGAGGAVTKLSHTAAQGGYFAATGTSDLHYGERANSLL
FAD
/(700)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry
PDB EntryTitleDetermination MethodResolutionR-Factor
41OQCThe crystal structure of augmenter of liver regeneration: a mammalian FAD dependent sulfhydryl oxidaseX-RAY1.800.202
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)
Show Details
1 / A   > Structure: HHHHLLH +15w
  > Sequence: REGRTWHFYECDICHNVNKLKFRW
FAD
/(126)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
2 / B   > Structure: HHHHLLH +12w
  > Sequence: REGRTWHFYECDICHNVNKLKFRW
FAD
/(126)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
3 / C   > Structure: HHHHLLH +11w
  > Sequence: REGRTWHFYCDICHNVNKLKFRW
FAD
/(126)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
4 / D   > Structure: HHHHLLH +13w
  > Sequence: REGRTWHFYECDICHNVNKLKFRW
FAD
/(126)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry
PDB EntryTitleDetermination MethodResolutionR-Factor
12F5VReaction geometry and thermostability mutant of pyranose 2-oxidase from the white-rot fungus Peniophora sp.X-RAY1.410.149
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)
Show Details
1 / A   > Structure: SLHLLHLLLLHLLLLSLLHLHLH +13w
  > Sequence: VGGPIDIILTRVGMSHWTCAVACTAGHLGCNPT
FAD
/(1625)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry
PDB EntryTitleDetermination MethodResolutionR-Factor
12F6CReaction geometry and thermostability of pyranose 2-oxidase from the white-rot fungus Peniophora sp., Thermostability mutant E542KX-RAY1.840.152
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)
Show Details
1 / A   > Structure: SLHLLLHLLLLHLLLLSLLHLLHLH +16w
  > Sequence: VGGPIDIGILTRVGMSHWTCAVACTAGHLHGCNPT
FAD
/(1625)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry
PDB EntryTitleDetermination MethodResolutionR-Factor
12I0ZCrystal structure of a FAD binding protein from Bacillus cereus, a putative NAD(FAD)-utilizing dehydrogenasesX-RAY1.840.198
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)
Show Details
1 / A   > Structure: SLLHLLLHHLLLSLLLHLHLLHH +14w
  > Sequence: IGGGPSDKGRKISGNTPVAVGVTGSDWFVGEGYNIA
FAD
/(501)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry
PDB EntryTitleDetermination MethodResolutionR-Factor
33MBGCrystal Structure of Human Augmenter of Liver Regeneration (ALR)X-RAY1.850.191
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)
Show Details
1 / A   > Structure: HHHHLLH +7w
  > Sequence: REGRSWHYCDLCHNVNKLKFRW
FAD
/(300)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
2 / B   > Structure: HHHHLLH +6w
  > Sequence: REGRSWHYCDLCHNVNKLKFRW
FAD
/(300)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
3 / C   > Structure: HHHHLLH +8w
  > Sequence: REGRSWHYCDLCHNVNKLKFRW
FAD
/(300)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry
PDB EntryTitleDetermination MethodResolutionR-Factor
43R7CThe structure of a hexahestidine-tagged form of augmenter of liver regeneration reveals a novel Cd(2)Cl(4)O(6) cluster that aids in crystal packingx-ray2.400.165
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)
Show Details
1 / A   > Structure: HHLLLLHHLLH +9w
  > Sequence: REGRTWHFYCCAEICHNVNLKFRW
FAD
/(126)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
2 / B   > Structure: HHLLLLHHLLH +11w
  > Sequence: REGRTWHFYCCAEICHNVNLKFVRW
FAD
/(126)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
3 / C   > Structure: HHHHLLH +3w
  > Sequence: REGRWHFYCICHNVNKLKFVRW
FAD
/(126)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
4 / D   > Structure: HHLLLLHHLLH +5w
  > Sequence: REGRTWHFYCCAEICHNVNLKFRW
FAD
/(126)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry
PDB EntryTitleDetermination MethodResolutionR-Factor
13TK0mutation of sfALRX-RAY1.610.182
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)
Show Details
1 / A   > Structure: HHHHLLH +17w
  > Sequence: REGRSWHYECDLCHNVNKLKFRW
FAD
/(300)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry
PDB EntryTitleDetermination MethodResolutionR-Factor
13U2MCrystal structure of human ALR mutant C142/145SX-RAY2.000.236
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)
Show Details
1 / A   > Structure: HHHHLLH +11w
  > Sequence: REGRSWHYSLCHNVNKLKFVRW
FAD
/(301)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry
PDB EntryTitleDetermination MethodResolutionR-Factor
13U5SSelenium Substituted Human Augmenter of Liver RegenerationX-RAY1.500.207
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)
Show Details
1 / A   > Structure: HHHHLLH +17w
  > Sequence: REGRSWHYDLHNVNKLKFRW
FAD
/(300)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry
PDB EntryTitleDetermination MethodResolutionR-Factor
14LDKFAD-linked sulfhydryl oxidase ALR mutationX-RAY2.040.198
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)
Show Details
1 / A   > Structure: HHHHLLH +9w
  > Sequence: REGRSWHYDLCHNVNKLKFRW
FAD
/(301)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry
PDB EntryTitleDetermination MethodResolutionR-Factor
11YQ3Avian respiratory complex ii with oxaloacetate and ubiquinoneX-RAY2.200.175
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)
Show Details
1 / A   > Structure: SLLHSLLHLLLSLLLLHLSLLLLH +10w
  > Sequence: VGAGGAVTKLSHTAAQGGYFAATGTDLHYGERANSLL
FAD
/(1001)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry
PDB EntryTitleDetermination MethodResolutionR-Factor
92VIGCRYSTAL STRUCTURE OF HUMAN SHORT-CHAIN ACYL COA DEHYDROGENASEX-ray1.900.199
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)
Show Details
1 / A   > Structure: SLLLLLSLSHLLLH +9w
  > Sequence: FLSNGSWITKTIIYETEIL
FAD
/(600)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
2 / B   > Structure: SLLLLLSLSHLLLH +5w
  > Sequence: FLSNGSWITKTIIYETEIL
FAD
/(600)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
3 / C   > Structure: SLLLLLSLSHLLH +7w
  > Sequence: FALSNGSWITKTIIYETEIL
FAD
/(600)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
4 / D   > Structure: SLLLLLS
  > Sequence: FALSNGSW
FAD
/(600)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
5 / D   > Structure: S
  > Sequence: W
FAD
/()
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
6 / E   > Structure: SLLLLLSLSHLLLH +9w
  > Sequence: FALSNGSWITKTIIYETEIL
FAD
/(600)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
7 / F   > Structure: SLLLLLSLSHLLLH +6w
  > Sequence: FLSNGSWITKTIIYETEIL
FAD
/(600)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
8 / G   > Structure: SLLLLLSLSHLLLH +6w
  > Sequence: FLSNGSWITKTIIYETEL
FAD
/(600)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
9 / H   > Structure: SLLLLLSLSHLLLH +8w
  > Sequence: FALSNGSWITKTIIYETEL
FAD
/(600)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry
PDB EntryTitleDetermination MethodResolutionR-Factor
22WBICrystal structure of human acyl-CoA dehydrogenase 11X-ray2.800.225
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)
Show Details
1 / A   > Structure: SLLLLLLSLSHLLH +1w
  > Sequence: FMTVASSWSVHVLAPEV
FAD
/(600)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
2 / B   > Structure: SLLLLLLSLSHLLLLH
  > Sequence: FMTVASSWSVHVLADGPEV
FAD
/(600)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry
PDB EntryTitleDetermination MethodResolutionR-Factor
13NF4Crystal structure of acyl-CoA dehydrogenase from Mycobacterium thermoresistibile bound to flavin adenine dinucleotideX-ray2.350.194
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)
Show Details
1 / A   > Structure: SLLLLSLSHLLH +5w
  > Sequence: YLSGSWTKTIIFTQIL
FAD
/(384)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry
PDB EntryTitleDetermination MethodResolutionR-Factor
43MPIStructure of the glutaryl-coenzyme A dehydrogenase glutaryl-CoA complexX-ray2.050.178
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)
Show Details
1 / A   > Structure: HSLLLLSLSHLH +11w
  > Sequence: MFITGSWISKTMVESNIM
FAD
/(400)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
2 / B   > Structure: HSLLLLSLSHLLH +2w
  > Sequence: MFITGSWISKTMVESNIM
FAD
/(400)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
3 / C   > Structure: HSLLLLSLSHLH +11w
  > Sequence: MFITGSWISKTMVESNIM
FAD
/(400)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
4 / D   > Structure: HSLLLLSLSHLLH +7w
  > Sequence: MFITGSWISKTMVESNIM
FAD
/(400)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry
PDB EntryTitleDetermination MethodResolutionR-Factor
43OWACrystal Structure of Acyl-CoA Dehydrogenase complexed with FAD from Bacillus anthracisX-ray1.970.164
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)
Show Details
1 / A   > Structure: SLLLLSLSHLHH +5w
  > Sequence: YLTGSWITKTIIFTEILQ
FAD
/(601)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
2 / B   > Structure: SLLLLSLHLHH +7w
  > Sequence: YLTGSWITKIIFTEILQ
FAD
/(601)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
3 / C   > Structure: SLLLLSLHLLHH +10w
  > Sequence: YLTGSWITIIIFETEILQ
FAD
/(601)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
4 / D   > Structure: SLLLLSLHLHH +6w
  > Sequence: YLTGSWITIIIFTEILQ
FAD
/(601)
[+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]