Structure of PDB 1yhu Chain V Binding Site BS03

Receptor Information
>1yhu Chain V (length=144) Species: 6426 (Riftia pachyptila) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DYVCGPLQRLKVKRQWAEAYGSGNSREEFGHFIWSHVFQHSPAARDMFKR
VRGDNIHTPAFRAHATRVLGGLDMCIALLDDEPVLNTQLAHLAKQHETRG
VEAAHYDTVNHAVMMGVENVIGSEVFDQDAWKPCLNVITNGIQG
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 V 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)		F48 R50 V51 H64 L92 Q95 H96 R99 V101 H105 Y106 I142
Binding residue
(residue number reindexed from 1)		F48 R50 V51 H64 L92 Q95 H96 R99 V101 H105 Y106 I142
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:0001666 response to hypoxia
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
UniProtP80592|GLBB_RIFPA Giant hemoglobins B chain

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