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 'PLP' ...
Ligand: IDFull NameFormula Chemistry
PLPPYRIDOXAL-5'-PHOSPHATEC8 H10 N O6 PPLP
There are 27 CoeSFMs:
Nbr of Motifs
per PDB entry		 PDB EntryTitleDetermination MethodResolutionR-Factor
11NRGStructure and Properties of Recombinant Human Pyridoxine-5'-Phosphate OxidaseX-RAY1.950.192
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)		Show Details
1 / A   > Structure: SLHHL +4w
  > Sequence: LKYRSQ 		PLP
/(320)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry		 PDB EntryTitleDetermination MethodResolutionR-Factor
11JNWActive Site Structure of E. coli pyridoxine 5'-phosphate Oxidase X-RAY2.070.178
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)		Show Details
1 / A   > Structure: LLHLL +2w
  > Sequence: RYRHP 		PLP
/(260)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry		 PDB EntryTitleDetermination MethodResolutionR-Factor
13HY8Crystal Structure of Human Pyridoxine 5'-Phosphate Oxidase R229W MutantX-RAY2.500.229
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)		Show Details
1 / A   > Structure: LSLHLH
  > Sequence: ELKYRPS 		PLP
/(350)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry		 PDB EntryTitleDetermination MethodResolutionR-Factor
11G76STRUCTURE OF ESCHERICHIA COLI PYRIDOXINE 5'-PHOSPHATE OXIDASE COMPLEXED WITH PYRIDOXAL 5'-PHOSPHATEX-RA2.200.217
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)		Show Details
1 / A   > Structure: SHLLS +3w
  > Sequence: LKYRQW 		PLP
/(260)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry		 PDB EntryTitleDetermination MethodResolutionR-Factor
12AQ6 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PYRIDO PHOSPHATE OXIDASE COMPLEXED WITH PYRIDOXAL 5'-PHOSPHATE X-ray1.700.19
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)		Show Details
1 / A   > Structure: SHS +8w
  > Sequence: QSNRAKR 		PLP
/(401)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry		 PDB EntryTitleDetermination MethodResolutionR-Factor
11RCQcrystal structure of alanine racemase from a pathogenic bacterium, Pseudomonas aeruginosa, contains both internal and external aldimine formsX-ray1.450.149
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)		Show Details
1 / A   > Structure: SHLLSLHLLHH +2w
  > Sequence: VKYLRMHNSPRPGIY 		PLP
/(358)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry		 PDB EntryTitleDetermination MethodResolutionR-Factor
21VP4Crystal structure of a putative aminotransferase (tm1131) from thermotoga maritima msb8X-ray1.820.180
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)		Show Details
1 / A   > Structure: HHSLSLLSLLL +1w
  > Sequence: GSQYYVNDPYTSKR 		PLP
/(501)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
2 / B   > Structure: HHSLLSLLSLLL +1w
  > Sequence: GSQYYVNDPYTSKR 		PLP
/(501)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry		 PDB EntryTitleDetermination MethodResolutionR-Factor
124ATQGABA-transaminase A1R958 in complex with external aldimine PLP-GABA adductX-ray2.750.204
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)		Show Details
1 / A   > Structure: HLLLSLLH +3w
  > Sequence: SGAYHEDVQK 		PLP
/(1456)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
2 / B   > Structure: HLLLSLLH +2w
  > Sequence: SGAYHEDVQK 		PLP
/(1456)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
3 / C   > Structure: HLLLSLLH +3w
  > Sequence: SGAYHEDVQK 		PLP
/(1456)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
4 / D   > Structure: HLLLSLLH +2w
  > Sequence: SGAYHEDVQK 		PLP
/(1456)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
5 / E   > Structure: HLLLSLLH +3w
  > Sequence: SGAYHEDVQK 		PLP
/(1456)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
6 / F   > Structure: HLLLLSLLH +6w
  > Sequence: SGAYHGEDVQK 		PLP
/(1456)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
7 / G   > Structure: HLLLSLLH
  > Sequence: SGAYHEDVQK 		PLP
/(1456)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
8 / H   > Structure: HLLLSLLH +1w
  > Sequence: SGAYHEDVQK 		PLP
/(1456)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
9 / I   > Structure: HLLLSLLH +1w
  > Sequence: SGAYHEDVQK 		PLP
/(1457)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
10 / J   > Structure: HLLLSLLH
  > Sequence: SGAYHEDVQK 		PLP
/(1456)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
11 / K   > Structure: HLLLSLLH +1w
  > Sequence: SGAYHEDVQK 		PLP
/(1456)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
12 / L   > Structure: HLLLSLLH +1w
  > Sequence: SGAYHEDVQK 		PLP
/(1456)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
Nbr of Motifs
per PDB entry		 PDB EntryTitleDetermination MethodResolutionR-Factor
71RFUCrystal structure of pyridoxal kinase complexed with ADP and PLPX-ray 2.800.230
Motif No./ChainMotifBound Ligand
/(Nbr. in PDB)		Show Details
1 / A   > Structure: SLHLLLLLH
  > Sequence: SVGHTYYVGTGD 		PLP
/(401)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
2 / B   > Structure: SLHSLLLLLH +1w
  > Sequence: SVGFHTYYVGTGD 		PLP
/(1401)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
3 / C   > Structure: SLHSLLLLLH
  > Sequence: SVGFHTYYVGTGD 		PLP
/(2401)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
4 / D   > Structure: SLLLLLLH
  > Sequence: SVHTYYVGTGD 		PLP
/(3401)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
5 / E   > Structure: SLHLLLLLH
  > Sequence: SVGHTYYVGTGD 		PLP
/(4401)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
6 / F   > Structure: SLSLLLLLH
  > Sequence: SVFHTYYVGTGD 		PLP
/(5401)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]
7 / G   > Structure: SLHLLLLLH
  > Sequence: SVGHTYYVGTGD 		PLP
/(6401)		 [+]
  > Graphics rep1: [+]
  > Graphics rep2: [+]