Structure of PDB 6zib Chain AAA Binding Site BS02

Receptor Information

>6zib Chain AAA (length=723) Species: 10116 (Rattus norvegicus)

PRGSHMAEYLRLPHSLAMIRLCNPPVNAVSPTVIREVRNGLQKAGSDHTV
KAIVICGANGNFCAGADIHGFSAFTPGLALGSLVDEIQRYQKPVLAAIQG
VALGGGLELALGCHYRIANAKARVGLPEVTLGILPGARGTQLLPRVVGVP
VALDLITSGKYLSADEALRLGILDAVVKSDPVEEAIKFAQKIIDKPIEPR
RIFNKPVPSLPNMDSVFAEAIAKVRKQYPGVLAPETCVRSIQASVKHPYE
VGIKEEEKLFMYLRASGQAKALQYAFFAEKSANKWSTPSGASWKTASAQP
VSSVGVLGLGTMGRGIAISFARVGISVVAVESDPKQLDAAKKIITFTLEK
EASRAHQNGQAKPKLRFSSSTKELSTVDLVVEAVFEDMNLKKKVFAELSA
LCKPGAFLCTNTSALNVDDIASSTDRPQLVIGTHFFSPAHVMRLLEVIPS
RYSSPTTIATVMSLSKKIGKIGVVVGNCYGFVGNRMLAPYYNQGFFLLEE
GSKPEDVDGVLEEFGFKMGPFRVSDLAGLDVGWKIRKGQGLTGPSLPPGT
PVRKRGNSRYSPLGDMLCEAGRFGQKTGKGWYQYDKPLGRIHKPDPWLST
FLSQYREVHHIEQRTISKEEILERCLYSLINEAFRILEEGMAARPEHIDV
IYLHGYGWPRHKGGPMFYAASVGLPTVLEKLQKYYRQNPDIPQLEPSDYL
RRLVAQGSPPLKEWQSLAGPHGS

Ligand information

• Ligand ID: NAI
• InChI: InChI=1S/C21H29N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2,5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,25)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
• InChIKey: BOPGDPNILDQYTO-NNYOXOHSSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
  CACTVS 3.341: NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
  CACTVS 3.341: NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
• Formula: C21 H29 N7 O14 P2
• Name: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE;
  NADH
• ChEMBL: CHEMBL1234616
• DrugBank: DB00157
• ZINC: ZINC000008215403
• PDB chain: 6zib Chain AAA Residue 902

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6zib CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-1 (RPMFE1) COMPLEXED WITH ACETOACETYL-COA AND NADH
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): G305 T306 M307 E326 S327 Q331 A380 V381 F382 E383 N408 H431
• Binding residue (residue number reindexed from 1): G310 T311 M312 E331 S332 Q336 A383 V384 F385 E386 N411 H434
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): A61 F66 G76 G100 E103 P122 E123 G131 K249 S410 H431 E443 N481
• Catalytic site (residue number reindexed from 1): A66 F71 G81 G105 E108 P127 E128 G136 K254 S413 H434 E446 N484
• 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:6zib, PDBe:6zib, PDBj:6zib
• PDBsum: 6zib
• UniProt: P07896|ECHP_RAT Peroxisomal bifunctional enzyme (Gene Name=Ehhadh)