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 'NAP' ...
Ligand: IDFull NameFormula Chemistry
NAPNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATEC21 H28 N7 O17 P3NAP
There are 18 CoeSFMs:
Nbr of Motifs
per PDB entry		 PDB EntryTitleDetermination MethodResolutionR-Factor
41SUWCrystal structure of a NAD kinase from Archaeoglobus fulgidus in complex with its substrate and product: Insights into the catalysis of NAD kinaseX-RAY2.450.213
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)		Show Details
1 / A   > Structure: HLLLSHHLLL +3w
  > Sequence: GDGLRVLNEITGYSDGQ 		NAP
/(3075)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
2 / B   > Structure: HLLLSHHLLL +4w
  > Sequence: GDGLRVLNEITGYSDGQ 		NAP
/(3076)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
3 / C   > Structure: HLLLSHHLLL +3w
  > Sequence: GDGLRVLNEITGYSDGQ 		NAP
/(3077)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
4 / D   > Structure: HLLLSHHLLL +7w
  > Sequence: GDGLRVLNEITGYSDGQ 		NAP
/(3078)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry		 PDB EntryTitleDetermination MethodResolutionR-Factor
21Z0UCrystal structure of a NAD kinase from Archaeoglobus fulgidus bound by NADPX-RAY2.000.214
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)		Show Details
1 / A   > Structure: HLLLSHHLLL +5w
  > Sequence: GDGLRRLNEITGYSDGQ 		NAP
/(3076)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
2 / B   > Structure: HLLLSHHLLL +4w
  > Sequence: GDGLRRLNEITGYSDGQ 		NAP
/(3077)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry		 PDB EntryTitleDetermination MethodResolutionR-Factor
11MARREFINED STRUCTURE OF HUMAN ALDOSE REDUCTASE COMPLEXED WITH THE POTENT INHIBITOR ZOPOLRESTATX-RAY1.800.180
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)		Show Details
1 / A   > Structure: LLLLLLLLLL
  > Sequence: GTWYSLSPKS 		NAP
/(350)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry		 PDB EntryTitleDetermination MethodResolutionR-Factor
24ZQBCrystal structure of NADP-dependent dehydrogenase from Rhodobactersphaeroides in complex with NADP and sulfatX-RAY1.850.177
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)		Show Details
1 / A   > Structure: LLLHLLLLHSLLLLLLLLLLHLLLLLLL +15w
  > Sequence: AGRMGLGELWSRSKLLPETFARDVHSARY 		NAP
/(401)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
2 / B   > Structure: LLLHLLLLHSLLLLLLLLLLHLLLLLLL +16w
  > Sequence: AGRMGLGELWSRSKLLPETFARDVHSARY 		NAP
/(401)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry		 PDB EntryTitleDetermination MethodResolutionR-Factor
24G62Crystal structure of IMPase/NADP phosphatase complexed with NADP and Ca2+X-RAY2.200.175
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)		Show Details
1 / A   > Structure: LSHHLHSLLH +9w
  > Sequence: EDIDGTANVGACNTND 		NAP
/(307)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
2 / B   > Structure: SHHLHSLLH +11w
  > Sequence: DIDGTANVGACNTND 		NAP
/(306)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry		 PDB EntryTitleDetermination MethodResolutionR-Factor
24GI2CROTONYL-COA CARBOXYLASE/REDUCTASEX-ray3.000.185
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)		Show Details
1 / A   > Structure: HHLLLLLHSLHLLLLLLLLL
  > Sequence: YWLTWGSGGLVISKRHCATTHFH 		NAP
/(502)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
2 / B   > Structure: HHLLLLLHSLHLLHLLLLLLL
  > Sequence: YWLTWGSGGLISKRHTCATTHFH 		NAP
/(501)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry		 PDB EntryTitleDetermination MethodResolutionR-Factor
24HNHThe crystal structure of a short-chain dehydrogenases/reductase (wide type) from Veillonella parvula DSM 2008 in complex with NADPX-ray1.580.176
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)		Show Details
1 / A   > Structure: LLHLHLLLLLHSHSLLSH +15w
  > Sequence: GAGQIRRSFGAEDVSYLTWLR 		NAP
/(301)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
2 / B   > Structure: LHLHLLLLLLHSHSLSH +19w
  > Sequence: AGQIRRSFQGAEDVSMYLTWLR 		NAP
/(302)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry		 PDB EntryTitleDetermination MethodResolutionR-Factor
34K6Fcrystal structure of a putative Acetoacetyl-CoA reductase from Burkholderia cenocepacia bound to the co-factor NADPX-ray1.500.168
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)		Show Details
1 / B   > Structure: LSLLLLLLLLH +5w
  > Sequence: GYSNVDVAGIT 		NAP
/(300)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
2 / C   > Structure: LHSLLLLLLLLLHSLHHSLLLH +23w
  > Sequence: GGGLYSNVDVNAGITISSYKPGYLTV 		NAP
/(300)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
3 / D   > Structure: LHSLLLLLLLLLHSLHHSLLLH +22w
  > Sequence: GGGLYSNVDVNAGITISSYKPGYLTV 		NAP
/(300)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]