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Structure of PDB 4ykf Chain A Binding Site BS02

Receptor Information
>4ykf Chain A (length=521) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLDTNMKTQLKAYLEKLTKPVELIATLDDSAKSAEIKELLAEIAELSDKV
TFKEDNSLPVRKPSFLITNPGSNQGPRFAGSPLGHEFTSLVLALLWTGGH
PSKEAQSLLEQIRHIDGDFEFETYYSLSCHNCPDVVQALNLMSVLNPRIK
HTAIDGGTFQNEITDRNVMGVPAVFVNGKEFGQGRMTLTEIVAKIDTGAE
KRAAEELNKRDAYDVLIVGSGPAGAAAAIYSARKGIRTGLMGERFGGQIL
DTVDIENYISVPKTEGQKLAGALKVHVDEYDVDVIDSQSASKLIPAAVEG
GLHQIETASGAVLKARSIIVATGAKWRNMNVPGEDQYRTKGVTYCPHCDG
PLFKGKRVAVIGGGNSGVEAAIDLAGIVEHVTLLEFAPEMKADQVLQDKL
RSLKNVDIILNAQTTEVKGDGSKVVGLEYRDRVSGDIHNIELAGIFVQIG
LLPNTNWLEGAVERNRMGEIIIDAKCETNVKGVFAAGDCTTVPYKQIIIA
TGEGAKASLSAFDYLIRTKTA
Ligand information
Ligand IDNAI
InChIInChI=1S/C21H29N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2,5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,25)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBOPGDPNILDQYTO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
FormulaC21 H29 N7 O14 P2
Name1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE;
NADH
ChEMBLCHEMBL1234616
DrugBankDB00157
ZINCZINC000008215403
PDB chain4ykf Chain A Residue 602 [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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PDB4ykf Crystallographic and solution studies of NAD(+)- and NADH-bound alkylhydroperoxide reductase subunit F (AhpF) from Escherichia coli provide insight into sequential enzymatic steps
Resolution2.5 Å
Binding residue
(original residue number in PDB)		I361 G364 N365 S366 E385 F386 K391 I449 M467
Binding residue
(residue number reindexed from 1)		I361 G364 N365 S366 E385 F386 K391 I449 M467
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) C345 C348 D349
Catalytic site (residue number reindexed from 1) C345 C348 D349
Enzyme Commision number 1.8.1.-
Gene Ontology
Molecular Function
GO:0004791 thioredoxin-disulfide reductase (NADPH) activity
GO:0008785 alkyl hydroperoxide reductase activity
GO:0016491 oxidoreductase activity
GO:0016668 oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor
GO:0050660 flavin adenine dinucleotide binding
GO:0051287 NAD binding
GO:0071949 FAD binding
Biological Process
GO:0000302 response to reactive oxygen species
GO:0006979 response to oxidative stress
GO:0042744 hydrogen peroxide catabolic process
GO:0045454 cell redox homeostasis
GO:0098869 cellular oxidant detoxification
Cellular Component
GO:0005829 cytosol
GO:0009321 alkyl hydroperoxide reductase complex

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4ykf, PDBe:4ykf, PDBj:4ykf
PDBsum4ykf
PubMed26092085
UniProtP35340|AHPF_ECOLI Alkyl hydroperoxide reductase subunit F (Gene Name=ahpF)

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