Structure of PDB 5l1n Chain B Binding Site BS02

Receptor Information
>5l1n Chain B (length=443) Species: 70601 (Pyrococcus horikoshii OT3) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKKKVVIIGGGAAGMSAASRVKRLKPEWDVKVFEATEWVSHAPCGIPYVV
EGLSTPDKLMAAGPEVFIKKRGIDLHLNAEVIEVDTGYVRVRENGGEKSY
EWDYLVFANGASPQVPAIEGVNLKGVFTADLPPDALAIREYMEKYKVENV
VIIGGGYIGIEMAEAFAAQGKNVTMIVRGERVLRRSFDKEVTDILEEKLK
KHVNLRLQEITMKIEGEERVEKVVTDAGEYKAELVILATGIKPNIELAKQ
LGVRIGETGAIWTNEKMQTSVENVYAAGDVAETRHVITGRRVWVPLAPAG
NKMGYVAGSNIAGKELHFPGVLGTAVTKFMDVEIGKTGLTEMEALKEGYD
VRTAFIKASTRPAYYPGGREIWLKGVVDNETNRLLGVQVVGSDILPRIDT
AAAMLMAGFTTKDAFFTDLAYAPPFAPVWDPLIVLARVLKFLE
Ligand information
Ligand IDFAD
InChIInChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
ACDLabs 10.04O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain5l1n Chain B Residue 901 [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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PDB5l1n A broader active site inPyrococcus horikoshiiCoA disulfide reductase accommodates larger substrates and reveals evidence of subunit asymmetry.
Resolution3.6 Å
Binding residue
(original residue number in PDB)		G13 G15 A16 A17 F37 E38 A39 H45 P47 C48 E84 V85 A133 D134 L135 Y161 G282 D283 L300 A301
Binding residue
(residue number reindexed from 1)		G9 G11 A12 A13 F33 E34 A35 H41 P43 C44 E80 V81 A129 D130 L131 Y157 G278 D279 L296 A297
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) A16 V43 P47 C48 S58 D61 Y161 E165 N305 A424 A426 P431
Catalytic site (residue number reindexed from 1) A12 V39 P43 C44 S54 D57 Y157 E161 N301 A420 A422 P427
Enzyme Commision number 1.8.1.-
1.8.1.14: CoA-disulfide reductase.
Gene Ontology
Molecular Function
GO:0003756 protein disulfide isomerase activity
GO:0016491 oxidoreductase activity
GO:0050451 CoA-disulfide reductase (NADPH) activity
GO:0050660 flavin adenine dinucleotide binding
GO:0050661 NADP binding

View graph for
Molecular Function
External links
PDB RCSB:5l1n, PDBe:5l1n, PDBj:5l1n
PDBsum5l1n
PubMed29988575
UniProtO58308|NCPPR_PYRHO NAD(P)H coenzyme A polysulfide/persulfide reductase (Gene Name=PH0572)

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