Structure of PDB 7d9f Chain B Binding Site BS02

Receptor Information
>7d9f Chain B (length=587) Species: 208964 (Pseudomonas aeruginosa PAO1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RYYPPALTGLRGSHPGAFEVAHQMGWEKKTFDVDHLPIEEEYDLVVVGGG
ISGLAAAWFYRERHPAARILVIENHDDFGGHAKRNEFQAGGRTILGYGGS
ESLQSPNALYSEDAKHLLKRLGVELKRFETAFDTDFYPGLGLSRAVFFDK
ASFGVDKLVSGDPTPMVADEVPRDRLNARSWRAFIGDFPLSREDREALIA
LYESPRDYLAGKSVEEKETYLAKTSYRDYLLKNVGLSETSVKYFQGRSND
FSALGADALPAADAYAAGFPGFDALGLPQPSEEAQAEMDEPYIYHFPDGN
ASLARLMVRDLIPAVAPGRGMEDIVMARFDYSKLDLAGHPVRLRLNSTAV
SVRNRAGGVDVGYSRAGRLHRVRGKHCVMACYNMMVPYLLRDLSEEQAHA
LSQNVKFPLVYTKVLLRNWQAWKTLGIHEIYAPTLPYSRIKLDFPVDLGS
YRHPRDPRQPIGVHMVYVPTTPNAGMDARTQARVGRSKLYAMSFEQLEKD
IRDQLQAMLGPAGFDHRRDITGITVNRWSHGYSYFMNTLYDDEAESEALM
ELARSKVGNVAIANSDAAWDAYAHAAIDQAVRAVREL
Ligand information
Ligand IDHEM
InChIInChI=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-;
InChIKeyKABFMIBPWCXCRK-RGGAHWMASA-L
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1c2n3c(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 3.385CC1=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 12.01C=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
FormulaC34 H32 Fe N4 O4
NamePROTOPORPHYRIN IX CONTAINING FE;
HEME
ChEMBL
DrugBankDB18267
ZINC
PDB chain7d9f Chain B Residue 703 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB7d9f Structure of Pseudomonas aeruginosa spermidine dehydrogenase: a polyamine oxidase with a novel heme-binding fold.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		S45 F50 A53 H54 W58 H107 Y414 M416 M417 Y420 R518 S519 Y522 R559 S561 H562
Binding residue
(residue number reindexed from 1)		S13 F18 A21 H22 W26 H75 Y382 M384 M385 Y388 R486 S487 Y490 R527 S529 H530
Annotation score1
Enzymatic activity
Enzyme Commision number 1.5.99.6: spermidine dehydrogenase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding

View graph for
Molecular Function
External links
PDB RCSB:7d9f, PDBe:7d9f, PDBj:7d9f
PDBsum7d9f
PubMed34741591
UniProtQ9HXS8

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