Structure of PDB 1kbi Chain A Binding Site BS01

Receptor Information
>1kbi Chain A (length=504) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EPKLDMNKQKISPAEVAKHNKPDDCWVVINGYVYDLTRFLPNHPGGQDVI
KFNAGKDVTAIFEPLHAPNVIDKYIAPEKKLGPLQGSMPPELVCPPYAPG
ETKEDIARKEQLKSLLPPLDNIINLYDFEYLASQTLTKQAWAYYSSGAND
EVTHRENHNAYHRIFFKPKILVDVRKVDISTDMLGSHVDVPFYVSATALC
KLGNPLEGEKDVARGCGQGVTKVPQMISTLASCSPEEIIEAAPSDKQIQW
YQLYVNSDRKITDDLVKNVEKLGVKALFVTVDAPSLGQREKDMKLKFSNT
KKTNVEESQGASRALSKFIDPSLTWKDIEELKKKTKLPIVIKGVQRTEDV
IKAAEIGVSGVVLSNHGGRQLDFSRAPIEVLAETMPILEQRNLKDKLEVF
VDGGVRRGTDVLKALCLGAKGVGLGRPFLYANSCYGRNGVEKAIEILRDE
IEMSMRLLGVTSIAELKPDLLDLSTLKARTVGVPNDVLYNEVYEGPTLTE
FEDA
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 chain1kbi Chain A Residue 760 [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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PDB1kbi Crystallographic study of the recombinant flavin-binding domain of Baker's yeast flavocytochrome b(2): comparison with the intact wild-type enzyme.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		F39 H43 P44 G45 V49 I50 V58 I61 F62 H66 V70 Y97 Q139 Y143 A198 L230 K296
Binding residue
(residue number reindexed from 1)		F39 H43 P44 G45 V49 I50 V58 I61 F62 H66 V70 Y97 Q139 Y143 A198 L230 K296
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) S228 Y254 T280 D282 K349 H373
Catalytic site (residue number reindexed from 1) S228 Y254 T280 D282 K342 H366
Enzyme Commision number 1.1.2.3: L-lactate dehydrogenase (cytochrome).
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0020037 heme binding

View graph for
Molecular Function
External links
PDB RCSB:1kbi, PDBe:1kbi, PDBj:1kbi
PDBsum1kbi
PubMed11914072
UniProtP00175|CYB2_YEAST L-lactate dehydrogenase (cytochrome) (Gene Name=CYB2)

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