Structure of PDB 1yhu Chain D Binding Site BS01

Receptor Information
>1yhu Chain D (length=149) Species: 6426 (Riftia pachyptila) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AASCTTEDRREMQLMWGNVWSAQFTGRRIAIAQAVFKDLFANVPDAVGLF
GAVKGDEVNSNEFKAHCIRVVNGLDSSIGLLSDPATLNEQLSHLATQHKA
RSGVTKGGFSAIAQSFLRVMPQVASCFNPDAWSRCFNRITTGMTEPLPA
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 chain1yhu Chain D Residue 160 [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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PDB1yhu Sulfide binding is mediated by zinc ions discovered in the crystal structure of a hydrothermal vent tubeworm hemoglobin.
Resolution3.15 Å
Binding residue
(original residue number in PDB)		F50 V53 H66 R69 V70 L74 Q97 H98 G108 F109 I112 M143
Binding residue
(residue number reindexed from 1)		F50 V53 H66 R69 V70 L74 Q97 H98 G108 F109 I112 M143
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005344 oxygen carrier activity
GO:0005506 iron ion binding
GO:0019825 oxygen binding
GO:0020037 heme binding
GO:0046872 metal ion binding
Biological Process
GO:0015671 oxygen transport
Cellular Component
GO:0005576 extracellular region
GO:0005833 hemoglobin complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1yhu, PDBe:1yhu, PDBj:1yhu
PDBsum1yhu
PubMed15710902
UniProtQ8IFJ9

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