Structure of PDB 6t88 Chain A Binding Site BS01

Receptor Information

>6t88 Chain A (length=454) Species: 211586 (Shewanella oneidensis MR-1)

MEYTYDVVIIGSGGAGFSAGLEAIAAGRSAVIIEKMPIIGGNSLISGAEM
NVAGSWVQKNMGITDSKELFISDTLKGGDFKGDPEMVKTMVDNAVGAAEW
LRDYVKVEFYPDQLFQFGGHSVKRALIPKGHTGAEVISKFSIKADEVGLP
IHTNTKAEKLIQDQTGRIVGVEAAHNGKTITYHAKRGVVIATGGFSSNME
MRKKYNPELDERYGSTGHAGGTGDGIVMAEKIHAAAKNMGYIQSYPICSP
TSGAIALIADSRFFGAVLINQKGERFVEELERRDVISHAILAQPGRYTYV
LWNQDIENVAHTVEMHQGELKEFTKDGLMYKVDTLEEAAKVFNIPEDKLL
STIKDVNHYAATGKDEAFNHRSGLVDLSKGPYWILKATPSVHHTMGGLVV
DTRTRVLDEQGKVIPGLFAAGEVTGLTHGTNRLGGNAYTDIIVYGRIAGQ
EAAK

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: 6t88 Chain A Residue 607

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6t88 Structural characterization of the microbial enzyme urocanate reductase mediating imidazole propionate production.
• Resolution: 1.4 Å
• Binding residue (original residue number in PDB): I138 G139 G141 A143 E162 K163 G169 N170 S171 S174 G175 A176 E177 A285 T320 G321 T344 H346 D352 H520 H521 G549 E550 G563 A565 Y566 I569
• Binding residue (residue number reindexed from 1): I10 G11 G13 A15 E34 K35 G41 N42 S43 S46 G47 A48 E49 A157 T192 G193 T216 H218 D224 H392 H393 G421 E422 G435 A437 Y438 I441
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): F245 Q371 Y373 A384 A387 R390 R411 H520 H521 R560
• Catalytic site (residue number reindexed from 1): F117 Q243 Y245 A256 A259 R262 R283 H392 H393 R432
• Enzyme Commision number: 1.3.99.33: urocanate reductase.

Gene Ontology

Molecular Function

• GO:0010181 FMN binding
• GO:0016491 oxidoreductase activity

External links

• PDB: RCSB:6t88, PDBe:6t88, PDBj:6t88
• PDBsum: 6t88
• PubMed: 33649331
• UniProt: Q8CVD0|URDA_SHEON Urocanate reductase (Gene Name=urdA)