Structure of PDB 8p02 Chain D Binding Site BS01

Receptor Information

>8p02 Chain D (length=514) Species: 96773 (Thauera chlorobenzoica)

ERVGEKDLRAALEWFRSKGYLVETNKEVNPDLEITGLQKIFDGSLPMLFN
NVKDMPHARAITNLFGDIRVVEELFGWENSLDRVKKVARAIDHPLKPVII
GQDEAPVQEEVLTTDLDVNKWLTAIRHTPLETEMTIGSGISCVVGPYFDG
GSHIGYNRMNFRWGNVGTFQISPGSHMWQVMTEHYKDDEPIPLTMCFGVP
PSCTYVAGAGFDYAILPKGCDEIGIAGAIQGSPVRLVKCRTIDAYTLADA
EYVLEGYLHPRDKRYETAESEAADIQGRFHFHPEWAGYMGKAYKAPTFHV
TAITMRRRESKPIIFPLGVHTADDANIDTSVRESAIFALCERLQPGIVQN
VHIPYCMTDWGGCIIQVKKRNQIEEGWQRNFLAAILACSQGMRLAIAVSE
DVDIYSMDDIMWCLTTRVNPQTDILNPLPGGRGQTFMPAERMTSGDKQWT
ASNTQFEGGMGIDATVPYGYESDFHRPVYGVDLVKPENFFDAKDIDKMKS
RMAGWVLSLARTGR

Ligand information

• Ligand ID: BYC
• InChI: InChI=1S/C28H40N7O17P3S/c1-28(2,22(38)25(39)31-9-8-18(36)30-10-11-56-27(40)16-6-4-3-5-7-16)13-49-55(46,47)52-54(44,45)48-12-17-21(51-53(41,42)43)20(37)26(50-17)35-15-34-19-23(29)32-14-33-24(19)35/h3-7,14-15,17,20-22,26,37-38H,8-13H2,1-2H3,(H,30,36)(H,31,39)(H,44,45)(H,46,47)(H2,29,32,33)(H2,41,42,43)/t17-,20-,21-,22+,26-/m1/s1
• InChIKey: VEVJTUNLALKRNO-TYHXJLICSA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCSC(=O)c4ccccc4)O
  ACDLabs 12.01: O=C(SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O)c4ccccc4
  OpenEye OEToolkits 1.7.0: CC(C)(CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCSC(=O)c4ccccc4)O
  CACTVS 3.370: CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCSC(=O)c4ccccc4
  CACTVS 3.370: CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[C@@H](O)C(=O)NCCC(=O)NCCSC(=O)c4ccccc4
• Formula: C28 H40 N7 O17 P3 S
• Name: benzoyl coenzyme A
• ZINC: ZINC000008551184
• PDB chain: 8p02 Chain D Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8p02 Cryo-EM structure of Phthaloyl-CoA decarboxylase (Pcd) bound with product, benzoyl-CoA
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): Q183 S185 P186 W191 T195 Y198 Q289 E297 W298 Y306 D372 W373 T448 F449 T463 A464
• Binding residue (residue number reindexed from 1): Q170 S172 P173 W178 T182 Y185 Q276 E284 W285 Y293 D359 W360 T435 F436 T450 A451
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0016831 carboxy-lyase activity

Biological Process

• GO:0033494 ferulate metabolic process
• GO:0046281 cinnamic acid catabolic process

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:8p02, PDBe:8p02, PDBj:8p02
• PDBsum: 8p02
• UniProt: A0A193DUB4