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BioLiP

Structure of PDB 1d4d Chain A Binding Site BS03

Receptor Information
>1d4d Chain A (length=560) Species: 70863 (Shewanella oneidensis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VLADFHGEMGGCDSCHVSDKGGVTNDNLTHENGQCVSCHGDLKELAAAAP
VSPHKSHLIGEIACTSCHKGHEKSVAYCDACHSFGFDMPFGGKWERKFVP
VDADKAAQDKAIAAGVKETTDVVIIGSGGAGLAAAVSARDAGAKVILLEK
EPIPGGNTKLAAGGMNAAETKPQAKLGIEDKKQIMIDDTMKGGRNINDPE
LVKVLANNSSDSIDWLTSMGADMTDVGRMGGASVNRSHRPTGGAGVGAHV
AQVLWDNAVKRGTDIRLNSRVVRILEDGKVTGVLVKGEYTGYYVIKADAV
VIAAGGFAKNNERVSKYDPKLKGFKATNHPGATGDGLDVALQAGAATRDL
QYIQAHPTYSPAGGVMITEAVRGNGAIVVNREGNRFMNEITTRDKASAAI
LQQKGESAYLVFDDSIRKSLKAIEGYVHLNIVKEGKTIEELAKQIDVPAA
ELAKTVTAYNGFVSGKDAQFERPDLPRELVVAPFYALEIAPAVHHTMGGL
VIDTKAEVKSEKTAKPITGLYAAGEVTGGVHGANRLGGNAISDIVTYGRI
AGASAAKFAK
Ligand information
Ligand IDHEC
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,9-12H2,1-6H3,(H,39,40)(H,41,42);/q-4;+4/b21-7?,22-8?,26-13-,29-14-,30-15-,31-16-;
InChIKeyHXQIYSLZKNYNMH-LJNAALQVSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)CCC1=C(C2=CC6=C(C(=C/C)\C5=CC4=C(C(\C3=Cc7c(c(c8C=C1N2[Fe](N34)(N56)n78)CCC(=O)O)C)=C/C)C)C)C
OpenEye OEToolkits 1.5.0CC=C1C(=C2C=C3C(=CC)C(=C4N3[Fe]56N2C1=Cc7n5c(c(c7C)CCC(=O)O)C=C8N6C(=C4)C(=C8CCC(=O)O)C)C)C
CACTVS 3.341C\C=C1/C(=C2C=C3N4C(=Cc5n6c(C=C7N8C(=C(C)\C7=C/C)C=C1N2[Fe@@]468)c(C)c5CCC(O)=O)C(=C3C)CCC(O)=O)C
CACTVS 3.341CC=C1C(=C2C=C3N4C(=Cc5n6c(C=C7N8C(=C(C)C7=CC)C=C1N2[Fe]468)c(C)c5CCC(O)=O)C(=C3C)CCC(O)=O)C
FormulaC34 H34 Fe N4 O4
NameHEME C
ChEMBL
DrugBank
ZINC
PDB chain1d4d Chain A Residue 603 [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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PDB1d4d Structure and mechanism of the flavocytochrome c fumarate reductase of Shewanella putrefaciens MR-1.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		A6 H9 C15 C18 H19 K23 G24 G25 K75 G76 H77 Y297
Binding residue
(residue number reindexed from 1)		A3 H6 C12 C15 H16 K20 G21 G22 K69 G70 H71 Y289
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) M235 Q362 H364 M374 E377 R380 R401 H503 H504 R544
Catalytic site (residue number reindexed from 1) M229 Q354 H356 M366 E369 R372 R393 H494 H495 R535
Enzyme Commision number 1.3.2.4: fumarate reductase (cytochrome).
Gene Ontology
Molecular Function
GO:0010181 FMN binding
GO:0016491 oxidoreductase activity

View graph for
Molecular Function
External links
PDB RCSB:1d4d, PDBe:1d4d, PDBj:1d4d
PDBsum1d4d
PubMed10581551
UniProtP83223|FCCA_SHEON Fumarate reductase (cytochrome) (Gene Name=fccA)

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