Structure of PDB 3gsi Chain A Binding Site BS03

Receptor Information

>3gsi Chain A (length=827) Species: 1665 (Arthrobacter globiformis)

TPRIVIIGAGIVGTNLADELVTRGWNNITVLDQGPLNMPGGSTSHAPGLV
FQTNPSKTMASFAKYTVEKLLSLTEDGVSCFNQVGGLEVATTETRLADLK
RKLGYAAAWGIEGRLLSPAECQELYPLLDGENILGGLHVPSDGLASAARA
VQLLIKRTESAGVTYRGSTTVTGIEQSGGRVTGVQTADGVIPADIVVSCA
GFWGAKIGAMIGMAVPLLPLAHQYVKTTPVPAQQGRNDQPNGARLPILRH
QDQDLYYREHGDRYGIGSYAHRPMPVDVDTLGAYAPETVSEHHMPSRLDF
TLEDFLPAWEATKQLLPALADSEIEDGFNGIFSFTPDGGPLLGESKELDG
FYVAEAVWVTHSAGVAKAMAELLTTGRSETDLGECDITRFEDVQLTPEYV
SETSQQNFVEIYDVLHPLQPRLSPRNLRVSPFHARHKELGAFFLEAGGWE
RPYWFEANAALLKEMPAEWLPPARDAWSGMFSSPIAAAEAWKTRTAVAMY
DMTPLKRLEVSGPGALKLLQELTTADLAKKPGAVTYTLLLDHAGGVRSAI
TVARLSEDTFQLGANGNIDTAYFERAARHQTQSGSATDWVQVRDTTGGTC
CIGLWGPLARDLVSKVSDDDFTNDGLKYFRAKNVVIGGIPVTAMRLSYVG
ELGWELYTSADNGQRLWDALWQAGQPFGVIAAGRAAFSSLRLEKGYRSWG
TDMTTEHDPFEAGLGFAVKMAKESFIGKGALEGRTEEASARRLRCLTIDD
GRSIVLGKEPVFYKEQAVGYVTSAAYGYTVAKPIAYSYLPGTVSVGDSVD
IEYFGRRITATVTEDPLYDPKMTRLRG

Ligand information

• Ligand ID: FAD
• InChI: InChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
• InChIKey: VWWQXMAJTJZDQX-UYBVJOGSSA-N
• SMILES:
  CACTVS 3.341: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
  OpenEye OEToolkits 1.5.0: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
  OpenEye OEToolkits 1.5.0: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
  CACTVS 3.341: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
  ACDLabs 10.04: O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
• Formula: C27 H33 N9 O15 P2
• Name: FLAVIN-ADENINE DINUCLEOTIDE
• ChEMBL: CHEMBL1232653
• DrugBank: DB03147
• ZINC: ZINC000008215434
• PDB chain: 3gsi Chain A Residue 902

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3gsi An internal reaction chamber in dimethylglycine oxidase provides efficient protection from exposure to toxic formaldehyde.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): G13 I14 V15 D35 Q36 G44 S45 T46 H48 P50 L52 T173 V174 A203 G204 W206 H225 Y259 G333 I334 F335 V360 W361 V362 T363
• Binding residue (residue number reindexed from 1): G10 I11 V12 D32 Q33 G41 S42 T43 H45 P47 L49 T170 V171 A200 G201 W203 H222 Y256 G330 I331 F332 V357 W358 V359 T360
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H225 Y259 A552
• Catalytic site (residue number reindexed from 1): H222 Y256 A549
• Enzyme Commision number: 1.5.3.10: dimethylglycine oxidase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0016491 oxidoreductase activity
• GO:0047866 dimethylglycine oxidase activity

External links

• PDB: RCSB:3gsi, PDBe:3gsi, PDBj:3gsi
• PDBsum: 3gsi
• PubMed: 19369258
• UniProt: Q9AGP8|DMGO_ARTGO Dimethylglycine oxidase (Gene Name=dmg)