Structure of PDB 3dy5 Chain A Binding Site BS02

Receptor Information

>3dy5 Chain A (length=1002) Species: 47982 (Plexaura homomalla)

WKNFGFEIFGEKYGQEELEKRIKDEHTPPPDSPVFGGLKLKLKKEKFKTL
FTLGTTLKGFRRATHTVGTGGIGEITIVNDPKFPEHEFFTAGRTFPARLR
HANLKYPDDAGADARSFSIKFADSDSDGPLDIVMNTGEANIFWNSPSLED
FVPVEEGDAAEEYVYKNPYYYYNLVEALRRAPDTFAHLYYYSQVTMPFKA
KDGKVRYCRYRALPGDVDIKEEDESGRLTEEEQRKIWIFSRHENEKRPDD
YLRKEYVERLQKGPVNYRLQIQIHEASPDDTATIFHAGILWDKETHPWFD
LAKVSIKTPLSPDVLEKTAFNIANQPASLGLLEAKSPEDYNSIGELRVAV
YTWVQHLRKLKIGSLNAIYNVEVETGDREHAGTDATITIRITGAKGRTDY
LKLFEAGSKEQYTVQGFDVGDIQLIELHSDGGGSGDPDWFVNRVIIISST
QDRVYSFPCFRWVIKDMVLFPGEATLPFNEVPAIVSEQRQKELEQRKLTY
QWDYVSDDMPGNIKAKTHDDLPRDVQFTDEKSRSYQESRKAALVNLGIGS
LWHEDRWFGYQFLNGANPVILTRCDALPSNFPVTNEHVNASLDRGKNLDE
EIKDGHIYIVDFKVLVGAKSYGGPVLEDIGEADIRYCAAPLALFYVNKLG
HLMPIAIQINQEPGPENPIWTPHEENEHDWMMAKFWLGVAESNFHQLNTH
LLRTHLTTESFALSTWRNLASAHPIFKLLQPHIYGVLAIDTIGRKELIGS
GGIVDQSLSLGGGGHVTFMEKCFKEVNLQDYHLPNALKKRGVDDPSKLPG
FYYRDDGLALWEAIETFIGEIIAIFYKNDDDVKRDNEIQSWIYDVHKNGW
RVNPGHQDHGVPASFESREQLKEVLTSLVFTFSCQHAAVNFSQKNAPAIL
RHPPPKKKGEATLQSILSTLPSKSQAAKAIATVYILTKFSEDERYLGNYS
ATAWEDKDALDAINRFQDKLEDISKKIKQRNENLEVPYIYLLPERIPNGT
AI

Ligand information

• Ligand ID: HEM
• InChI: InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
• InChIKey: KABFMIBPWCXCRK-RGGAHWMASA-L
• SMILES:
  OpenEye OEToolkits 1.7.6: Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
  CACTVS 3.385: CC1=C(CCC(O)=O)C2=Cc3n4[Fe]5|6|N2=C1C=c7n5c(=CC8=N|6C(=Cc4c(C)c3CCC(O)=O)C(=C8C=C)C)c(C)c7C=C
  ACDLabs 12.01: C=1c3c(c(c4C=C5C(=C(C=6C=C7C(=C(C8=CC=2C(=C(C=1N=2[Fe](n34)(N5=6)N78)CCC(=O)O)C)\C=C)C)\C=C)C)C)CCC(=O)O
• Formula: C34 H32 Fe N4 O4
• Name: PROTOPORPHYRIN IX CONTAINING FE;
  HEME
• DrugBank: DB18267
• PDB chain: 3dy5 Chain A Residue 1100

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3dy5 A covalent linker allows for membrane targeting of an oxylipin biosynthetic complex.
• Resolution: 3.51 Å
• Binding residue (original residue number in PDB): R64 T66 H67 R102 S120 M136 N137 F144 Q195 F322 R349 Y353 Q357 R360
• Binding residue (residue number reindexed from 1): R62 T64 H65 R100 S118 M134 N135 F142 Q193 F320 R347 Y351 Q355 R358
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): T66 H67 N137 Y353 H757 H762 H943 N947 I1066
• Catalytic site (residue number reindexed from 1): T64 H65 N135 Y351 H700 H705 H886 N890 I1002
• Enzyme Commision number: 1.13.11.40: arachidonate 8-lipoxygenase.
  4.2.1.-

Gene Ontology

Molecular Function

• GO:0005506 iron ion binding
• GO:0009978 allene oxide synthase activity
• GO:0016702 oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
• GO:0016829 lyase activity
• GO:0020037 heme binding
• GO:0046872 metal ion binding
• GO:0047677 arachidonate 8(R)-lipoxygenase activity
• GO:0051213 dioxygenase activity

Biological Process

• GO:0006631 fatty acid metabolic process
• GO:0006633 fatty acid biosynthetic process
• GO:0019369 arachidonate metabolic process
• GO:0031408 oxylipin biosynthetic process
• GO:0034440 lipid oxidation

Cellular Component

• GO:0005737 cytoplasm
• GO:0016020 membrane

External links

• PDB: RCSB:3dy5, PDBe:3dy5, PDBj:3dy5
• PDBsum: 3dy5
• PubMed: 18785758
• UniProt: O16025|AOSL_PLEHO Allene oxide synthase-lipoxygenase protein