Structure of PDB 4ydd Chain E Binding Site BS04

Receptor Information
>4ydd Chain E (length=892) Species: 640081 (Azospira oryzae PS) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AFEYSGWENFHRTQWSWDKKTRGAHLVNCTGACPHFVYSKDGVVMREEQS
KDIAPMPNIPEYNPRGCNKGECGHDYMYGPHRIKYPLIRVGERGEGKWRR
ATWEEALDMIADKCVDTIKNHAPDCISVYSPVPAVSPVSFSAGHRFAHYI
GAHAHTFYDWYGDHPTGQTQTCGVQGDTCETADWFNSKYIILWGSNPTQT
RIPDAHFLSEAQLNGAKIVSISPDYNSSTIKVDKWIHPQPGTDGALAMAM
AHVIIKEKLYDAHSLKEQTDLSYLVRSDTKRFLREADVVAGGSKDKFYFW
NAKTGKPVIPKGSWGDQPEKKGSPVGFLGRNTFAFPKGYIDLGDLDPALE
GKFNMQLLDGKTVEVRPVFEILKSRLMADNTPEKAAKITGVTAKAITELA
REFATAKPSMIICGGGTQHWYYSDVLLRAMHLLTALTGTEGTNGGGMNHY
IGQWKPAFVAGLVALAFPEGVNKQRFCQTTIWTYIHAEVNDEIISSDIDT
EKYLRDSITTGQMPNMPEQGRDPKVFFVYRGNWLNQAKGQKYVLENLWPK
LELIVDINIRMDSTALYSDVVLPSAHWYEKLDLNVTSEHSYINMTEPAIK
PMWESKTDWQIFLALAKRVEMAAKRKKYEKFNDEKFKWVRDLSNLWNQMT
MDGKLAEDEAAAQYILDNAPQSKGITIQMLREKPQRFKSNWTSPLKEGVP
YTPFQYFVVDKKPWPTLTGRQQFYLDHDTFFDMGVELPTYKAPIDADKYP
FRFNSPHSRHSVHSTFKDNVLMLRLQRGGPSIEMSPLDAKPLGIKDNDWV
EAWNNHGKVICRVKIRNGEQRGRVSMWHCPELYMDLLTGGSQSVCPVRIN
PTNLVGNYGHLFFRPNYYGPAGSQRDVRVNVKRYIGATPISF
Ligand information
Ligand IDMD1
InChIInChI=1S/C20H26N10O13P2S2/c21-19-26-14-8(16(34)28-19)25-5(1-23-14)12(46)13(47)6(31)2-40-44(36,37)43-45(38,39)41-3-7-10(32)11(33)18(42-7)30-4-24-9-15(30)27-20(22)29-17(9)35/h1,4-7,10-11,18,25,31-33,46-47H,2-3H2,(H,36,37)(H,38,39)(H3,21,26,28,34)(H3,22,27,29,35)/b13-12-/t5-,6-,7-,10-,11-,18-/m1/s1
InChIKeyIRGDLSAXQOKWLX-XHEYTWMPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.5c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OC[C@H](/C(=C(\[C@H]4C=NC5=C(N4)C(=O)NC(=N5)N)/S)/S)O)O)O)N=C(NC2=O)N
ACDLabs 10.04O=C2NC(=NC=1N=CC(NC=12)C(/S)=C(/S)C(O)COP(=O)(O)OP(=O)(O)OCC5OC(n4cnc3c4N=C(N)NC3=O)C(O)C5O)N
CACTVS 3.385NC1=NC2=C(N[CH](C=N2)C(S)=C(S)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5C(=O)NC(=Nc45)N)C(=O)N1
CACTVS 3.385NC1=NC2=C(N[C@H](C=N2)C(\S)=C(S)/[C@H](O)CO[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5C(=O)NC(=Nc45)N)C(=O)N1
OpenEye OEToolkits 1.7.5c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC(C(=C(C4C=NC5=C(N4)C(=O)NC(=N5)N)S)S)O)O)O)N=C(NC2=O)N
FormulaC20 H26 N10 O13 P2 S2
NamePHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER
ChEMBL
DrugBank
ZINCZINC000195826882
PDB chain4ydd Chain E Residue 1004 [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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PDB4ydd Perchlorate Reductase Is Distinguished by Active Site Aromatic Gate Residues.
Resolution1.86 Å
Binding residue
(original residue number in PDB)
Y168 D170 H426 R537 G538 N539 Q543 I564 N565 R567 D569 S581 K587 D615 S762 H764 H770 S771 T772 H835 Q849 Q881
Binding residue
(residue number reindexed from 1)
Y161 D163 H419 R530 G531 N532 Q536 I557 N558 R560 D562 S574 K580 D608 S755 H757 H763 S764 T765 H828 Q842 Q874
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K76 P138 P140 W167 Y168 D170 P172 Y457 Q460
Catalytic site (residue number reindexed from 1) K69 P131 P133 W160 Y161 D163 P165 Y450 Q453
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0043546 molybdopterin cofactor binding
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0009061 anaerobic respiration
GO:0045333 cellular respiration
Cellular Component
GO:0016020 membrane
GO:1990204 oxidoreductase complex

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:4ydd, PDBe:4ydd, PDBj:4ydd
PDBsum4ydd
PubMed26940877
UniProtG8QM55

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