Structure of PDB 6by0 Chain B Binding Site BS01

Receptor Information
>6by0 Chain B (length=721) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LAPEDGSHRPAAEPTPPGAQPTAPGSLKAPDTRNEKLNSLEDVRKGSENY
ALTTNQGVRIADDQNSLRAGSRGPTLLEDFILREKITHFDHERIPERIVH
ARGSAAHGYFQPYKSLSDITKADFLSDPNKITPVFVRFSTVQGGAGSADT
VRDIRGFATKFYTEEGIFDLVGNNTPIFFIQDAHKFPDFVHAVKPEPHWA
IPQGQSAHDTFWDYVSLQPETLHNVMWAMSDRGIPRSYRTMEGFGIHTFR
LINAEGKATFVRFHWKPLAGKASLVWDEAQKLTGRDPDFHRRELWEAIEA
GDFPEYELGFQLIPEEDEFKFDFDLLDPTKLIPEELVPVQRVGKMVLNRN
PDNFFAENEQAAFHPGHIVPGLDFTNDPLLQGRLFSYTDTQISRLGGPNF
HEIPINRPTCPYHNFQRDGMHRMGIDTNPANYEPNSINDNWPRETPPGPK
RGGFESYQERVEGNKVRERSPSFGEYYSHPRLFWLSQTPFEQRHIVDGFS
FELSKVVRPYIRERVVDQLAHIDLTLAQAVAKNLGIELTDDQLNITPPPD
VNGLKKDPSLSLYAIPDGDVKGRVVAILLNDEVRSADLLAILKALKAKGV
HAKLLYSRMGEVTADDGTVLPIAATFAGAPSLTVDAVIVPCGNIADIADN
GDANYYLMEAYKHLKPIALAGDARKFKATIKIEEGIVEADSADGSFMDEL
LTLMAAHRVWSRIPKIDKIPA
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 chain6by0 Chain B Residue 801 [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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PDB6by0 SIMBAD: a sequence-independent molecular-replacement pipeline.
Resolution2.93 Å
Binding residue
(original residue number in PDB)		R125 V127 H128 R165 V199 G200 N201 F206 F214 I274 F391 L407 R411 S414 Y415 T418 Q419 R422
Binding residue
(residue number reindexed from 1)		R97 V99 H100 R137 V171 G172 N173 F178 F186 I246 F363 L379 R383 S386 Y387 T390 Q391 R394
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H128 N201 H392
Catalytic site (residue number reindexed from 1) H100 N173 H364
Enzyme Commision number 1.11.1.6: catalase.
Gene Ontology
Molecular Function
GO:0004096 catalase activity
GO:0004601 peroxidase activity
GO:0005506 iron ion binding
GO:0020037 heme binding
GO:0042802 identical protein binding
GO:0046872 metal ion binding
Biological Process
GO:0006972 hyperosmotic response
GO:0006974 DNA damage response
GO:0006979 response to oxidative stress
GO:0042744 hydrogen peroxide catabolic process
GO:0098869 cellular oxidant detoxification
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6by0, PDBe:6by0, PDBj:6by0
PDBsum6by0
PubMed29968670
UniProtP21179|CATE_ECOLI Catalase HPII (Gene Name=katE)

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