Structure of PDB 6z5v Chain AAA Binding Site BS01

Receptor Information

>6z5v Chain AAA (length=719) Species: 10116 (Rattus norvegicus)

GSHMAEYLRLPHSLAMIRLCNPPVNAVSPTVIREVRNGLQKAGSDHTVKA
IVICGANGNFCAGADIHGFSAFTPGLALGSLVDEIQRYQKPVLAAIQGVA
LGGGLELALGCHYRIANAKARVGLPEVTLGILPGARGTQLLPRVVGVPVA
LDLITSGKYLSADEALRLGILDAVVKSDPVEEAIKFAQKIIDKPIEPRRI
FNKPVPSLPNMDSVFAEAIAKVRKQYPGVLAPETCVRSIQASVKHPYEVG
IKEEEKLFMYLRASGQAKALQYAFFAEKSANKWSTPSGASWKTASAQPVS
SVGVLGLGTMGRGIAISFARVGISVVAVESDPKQLDAAKKIITFTLEKEA
SRAHQSAKPKLRFSSSTKELSTVDLVVEAVFEDMNLKKKVFAELSALCKP
GAFLCTNTSALNVDDIASSTDRPQLVIGTHFFSPAHVMRLLEVIPSRYSS
PTTIATVMSLSKKIGKIGVVVGNCYGFVGNRMLAPYYNQGFFLLEEGSKP
EDVDGVLEEFGFKMGPFRVSDLAGLDVGWKIRKGQGLTGPSLPPGTPVRK
RGNSRYSPLGDMLCEAGRFGQKTGKGWYQYDKPLGRIHKPDPWLSTFLSQ
YREVHHIEQRTISKEEILERCLYSLINEAFRILEEGMAARPEHIDVIYLH
GYGWPRHKGGPMFYAASVGLPTVLEKLQKYYRQNPDIPQLEPSDYLRRLV
AQGSPPLKEWQSLAGPHGS

Ligand information

• Ligand ID: NAD
• InChI: InChI=1S/C21H27N7O14P2/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/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
• InChIKey: BAWFJGJZGIEFAR-NNYOXOHSSA-N
• SMILES:
  CACTVS 3.341: NC(=O)c1ccc[n+](c1)[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: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
  CACTVS 3.341: NC(=O)c1ccc[n+](c1)[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
  OpenEye OEToolkits 1.5.0: c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
• Formula: C21 H27 N7 O14 P2
• Name: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
• ChEMBL: CHEMBL1234613
• DrugBank: DB14128
• PDB chain: 6z5v Chain AAA Residue 1001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6z5v Crystallographic binding studies of rat peroxisomal multifunctional enzyme type 1 with 3-ketodecanoyl-CoA: capturing active and inactive states of its hydratase and dehydrogenase catalytic sites.
• Resolution: 2.33 Å
• Binding residue (original residue number in PDB): G303 G305 T306 M307 E326 S327 Q331 A380 V381 F382 E383 K388 N408 S410 H431
• Binding residue (residue number reindexed from 1): G306 G308 T309 M310 E329 S330 Q334 A379 V380 F381 E382 K387 N407 S409 H430
• 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): A64 F69 G79 G103 E106 P125 E126 G134 K252 S409 H430 E442 N480
• 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:6z5v, PDBe:6z5v, PDBj:6z5v
• PDBsum: 6z5v
• PubMed: 33263331
• UniProt: P07896|ECHP_RAT Peroxisomal bifunctional enzyme (Gene Name=Ehhadh)