Structure of PDB 2y4e Chain A Binding Site BS01

Receptor Information
>2y4e Chain A (length=384) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SAPGTLSPDARNEKQPFYGEHQAGILTPQQAAMMLVAFDVLASDKADLER
LFRLLTQRFAFLTQGGAAPETPNPRLPPLDSGILGGYIAPDNLTITLSVG
HSLFDERFGLAPQMPKKLQKMTRFPNDSLDAALCHGDVLLQICANTQDTV
IHALRDIIKHTPDLLSVRWKREGFISDHAARSKGKETPINLLGFKDGTAN
PDSQNDKLMQKVVWVTADQQEPAWTIGGSYQAVRLIQFRVEFWDRTPLKE
QQTIFGRDKQTGAPLGMQHEHDVPDYASDPEGKVIALDSHIRLANPRTAE
SESSLMLRRGYSYSLGVTNSGQLDMGLLFVCYQHDLEKGFLTVQKRLNGE
ALEEYVKPIGGGYFFALPGVKDANDYFGSALLRV
Ligand information
Ligand IDPP9
InChIInChI=1S/C34H34N4O4/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/h7-8,13-16,36-37H,1-2,9-12H2,3-6H3,(H,39,40)(H,41,42)/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-
InChIKeyFEDYMSUPMFCVOD-UJJXFSCMSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1c2[nH]c(cc3nc(cc4[nH]c(cc5nc(c2)c(C)c5C=C)c(C)c4C=C)c(C)c3CCC(O)=O)c1CCC(O)=O
OpenEye OEToolkits 1.5.0Cc1c2cc3nc(cc4c(c(c([nH]4)cc5nc(cc(c1CCC(=O)O)[nH]2)C(=C5C)CCC(=O)O)C=C)C)C(=C3C)C=C
ACDLabs 10.04O=C(O)CCc5c2nc(cc4nc(cc1c(c(\C=C)c(n1)cc3nc(c2)C(=C3C)CCC(=O)O)C)C(\C=C)=C4C)c5C
OpenEye OEToolkits 1.5.0Cc1c2\cc\3/nc(\cc/4\c(c(/c(/[nH]4)c/c5n/c(c\c(c1CCC(=O)O)[nH]2)/C(=C5C)CCC(=O)O)C=C)C)C(=C3C)C=C
FormulaC34 H34 N4 O4
NamePROTOPORPHYRIN IX
ChEMBLCHEMBL1618319
DrugBank
ZINC
PDB chain2y4e Chain A Residue 1389 [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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PDB2y4e Efeb, the Peroxidase Component of the Efeuob Bacterial Fe(II) Transport System, Also Shows Novel Removal of Iron from Heme
Resolution2.3 Å
Binding residue
(original residue number in PDB)		N194 K199 D200 G201 T202 A203 F259 R261 H294 I295 N299 M310 R312 F333 F344 V347 Q348 L351 L356 V360
Binding residue
(residue number reindexed from 1)		N190 K195 D196 G197 T198 A199 F255 R257 H290 I291 N295 M306 R308 F329 F340 V343 Q344 L347 L352 V356
Annotation score3
Enzymatic activity
Enzyme Commision number 1.11.1.-
4.98.1.1: protoporphyrin ferrochelatase.
Gene Ontology
Molecular Function
GO:0004325 ferrochelatase activity
GO:0004601 peroxidase activity
GO:0016829 lyase activity
GO:0020037 heme binding
GO:0046872 metal ion binding
Biological Process
GO:0006974 DNA damage response
GO:0033212 iron import into cell
GO:0098869 cellular oxidant detoxification
Cellular Component
GO:0005829 cytosol
GO:0030288 outer membrane-bounded periplasmic space
GO:0042597 periplasmic space

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2y4e, PDBe:2y4e, PDBj:2y4e
PDBsum2y4e
PubMed
UniProtP31545|EFEB_ECOLI Deferrochelatase (Gene Name=efeB)

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