Structure of PDB 5jfm Chain C Binding Site BS01

Receptor Information

>5jfm Chain C (length=439) Species: 316056 (Rhodopseudomonas palustris BisB18)

VSDGVFETMDAAVEAAALAQQQYLLCSMSDRARFVQGIRDVILNQDTLEK
MSRMAVEETGMGNYEHKLIKNRLAGEKTPGIEDLTTDAFSGDNGLTLVEY
SPFGVIGAITPTTNPTETIVCNSIGMLAAGNSVVFSPHPRARQVSLLLVR
LINQKLAALGAPENLVVTVEKPSIENTNAMMAHPKVRMLVATGGPAIVKA
VLSTGKKAIGAGAGNPPVVVDETANIEKAACDIVNGCSFDNNLPCVAEKE
IIAVAQIADYLIFNLKKNGAYEIKDPAVLQQLQDLVLTAKGGPQTKCVGK
SAVWLLSQIGISVDASIKIILMEVPREHPFVQEELMMPILPLVRVETVDD
AIDLAIEVEHDNRHTAIMHSTDVRKLTKMAKLIQTTIFVKNGPSYAGLGA
GGEGYSTFTIAGPTGEGLTSAKSFARRRKCVMVEALNIR

Ligand information

• Ligand ID: 1VU
• InChI: InChI=1S/C24H40N7O17P3S/c1-4-15(33)52-8-7-26-14(32)5-6-27-22(36)19(35)24(2,3)10-45-51(42,43)48-50(40,41)44-9-13-18(47-49(37,38)39)17(34)23(46-13)31-12-30-16-20(25)28-11-29-21(16)31/h11-13,17-19,23,34-35H,4-10H2,1-3H3,(H,26,32)(H,27,36)(H,40,41)(H,42,43)(H2,25,28,29)(H2,37,38,39)/t13-,17-,18-,19+,23-/m1/s1
• InChIKey: QAQREVBBADEHPA-IEXPHMLFSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: CCC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
  CACTVS 3.385: CCC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(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
  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)CC
  CACTVS 3.385: CCC(=O)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
  OpenEye OEToolkits 1.7.6: CCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
• Formula: C24 H40 N7 O17 P3 S
• Name: propionyl Coenzyme A
• DrugBank: DB02912
• ZINC: ZINC000008551120
• PDB chain: 5jfm Chain C Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5jfm In Vitro Characterization and Concerted Function of Three Core Enzymes of a Glycyl Radical Enzyme - Associated Bacterial Microcompartment.
• Resolution: 2.516 Å
• Binding residue (original residue number in PDB): I194 P196 T197 T198 N199 S221 P222 H223 R225 S258 T262 T277 G278 C330 T380 M421 F493
• Binding residue (residue number reindexed from 1): I109 P111 T112 T113 N114 S136 P137 H138 R140 S173 T177 T192 G193 C245 T295 M336 F408
• Annotation score: 3

Enzymatic activity

• Catalytic site (original residue number in PDB): T198 A296 C330
• Catalytic site (residue number reindexed from 1): T113 A211 C245

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0008774 acetaldehyde dehydrogenase (acetylating) activity
• GO:0016491 oxidoreductase activity
• GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor

External links

• PDB: RCSB:5jfm, PDBe:5jfm, PDBj:5jfm
• PDBsum: 5jfm
• PubMed: 28202954
• UniProt: Q21A49