Structure of PDB 5omo Chain B Binding Site BS01

Receptor Information

>5omo Chain B (length=718) Species: 10116 (Rattus norvegicus)

HMAEYLRLPHSLAMIRLCNPPVNAVSPTVIREVRNGLQKAGSDHTVKAIV
ICGANGNFCAGADIHGFSAFTPGLALGSLVDEIQRYQKPVLAAIQGVALG
GGLELALGCHYRIANAKARVGLPEVTLGILPGARGTQLLPRVVGVPVALD
LITSGKYLSADEALRLGILDAVVKSDPVEEAIKFAQKIIDKPIEPRRIFN
KPVPSLPNMDSVFAEAIAKVRKQYPGVLAPETCVRSIQASVKHPYEVGIK
EEEKLFMYLRASGQAKALQYAFFAEKSANKWSTPSGASWKTASAQPVSSV
GVLGLGTMGRGIAISFARVGISVVAVESDPKQLDAAKKIITFTLEKEASR
AHQNGQASAKPKLRFSSSTKELSTVDLVVEAVFEDMNLKKKVFAELSALC
KPGAFLCTNTSALNVDDIASSTDRPQLVIGTHFFSPAHVMRLLEVIPSRY
SSPTTIATVMSLSKKIGKIGVVVGNCYGFVGNRMLAPYYNQGFFLLEEGS
KPEDVDGVLEEFGFKMGPFRVSDLAGLDVGWKIRKGQGLTGPSLPPGTPV
RKRGNSRYSPLGDMLCEAGRFGQKTGKGWYQYDKPLGRIHKPDPWLSTFL
SQYREVHHIEQRTISKEEILERCLYSLINEAFRILEEGMAARPEHIDVIY
LHGYGWPRHKGGPMFYAASVGLPTVLEKLQKYYRQNPDIPQLEPSDYLRR
LVAQGSPPLKEWQSLAGP

Ligand information

• Ligand ID: HSC
• InChI: InChI=1S/C31H54N7O18P3S/c1-4-5-6-7-8-9-19(39)14-22(41)60-13-12-33-21(40)10-11-34-29(44)26(43)31(2,3)16-53-59(50,51)56-58(48,49)52-15-20-25(55-57(45,46)47)24(42)30(54-20)38-18-37-23-27(32)35-17-36-28(23)38/h17-20,24-26,30,39,42-43H,4-16H2,1-3H3,(H,33,40)(H,34,44)(H,48,49)(H,50,51)(H2,32,35,36)(H2,45,46,47)/p-4/t19-,20+,24+,25+,26-,30+/m0/s1
• InChIKey: HIVSMYZAMUNFKZ-PNPVFPMQSA-J
• SMILES:
  CACTVS 3.370: CCCCCCC[C@H](O)CC(=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
  OpenEye OEToolkits 1.7.2: CCCCCCC[C@@H](CC(=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)O
  CACTVS 3.370: CCCCCCC[CH](O)CC(=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 1.7.2: CCCCCCCC(CC(=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)O
• Formula: C31 H50 N7 O18 P3 S
• Name: (S)-3-HYDROXYDECANOYL-COA
• PDB chain: 5omo Chain B Residue 805

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5omo CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE 1 (RPMFE1) COMPLEXED WITH 3S-HYDROXY-DECANOYL-COA AND 3- KETO-DECANOYL-COA
• Resolution: 2.49 Å
• Binding residue (original residue number in PDB): P20 V21 A59 G60 A61 D62 I63 F66 L98 G100 E103 P122 E123 L126 G131 Y156 F255 F271 K275 K279
• Binding residue (residue number reindexed from 1): P21 V22 A60 G61 A62 D63 I64 F67 L99 G101 E104 P123 E124 L127 G132 Y157 F256 F272 K276 K280
• Annotation score: 5

Enzymatic activity

• Catalytic site (original residue number in PDB): A61 F66 G76 G100 E103 P122 E123 P130 G131 K249 S410 H431 E443 N481
• Catalytic site (residue number reindexed from 1): A62 F67 G77 G101 E104 P123 E124 P131 G132 K250 S411 H432 E444 N482
• Enzyme Commision number: 1.1.1.35: 3-hydroxyacyl-CoA dehydrogenase.
  4.2.1.17: enoyl-CoA hydratase.
  5.3.3.8: Delta(3)-Delta(2)-enoyl-CoA isomerase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0003857 3-hydroxyacyl-CoA dehydrogenase activity
• GO:0004165 delta(3)-delta(2)-enoyl-CoA isomerase activity
• GO:0004300 enoyl-CoA hydratase activity
• GO:0016491 oxidoreductase activity
• GO:0016509 long-chain-3-hydroxyacyl-CoA dehydrogenase activity
• GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
• GO:0016829 lyase activity
• GO:0016853 isomerase activity
• GO:0016863 intramolecular oxidoreductase activity, transposing C=C bonds
• GO:0019899 enzyme binding
• GO:0070403 NAD+ binding

Biological Process

• GO:0006631 fatty acid metabolic process
• GO:0006635 fatty acid beta-oxidation

Cellular Component

• GO:0005777 peroxisome
• GO:0005829 cytosol

External links

• PDB: RCSB:5omo, PDBe:5omo, PDBj:5omo
• PDBsum: 5omo
• UniProt: P07896|ECHP_RAT Peroxisomal bifunctional enzyme (Gene Name=Ehhadh)