Structure of PDB 4ydd Chain A Binding Site BS03

Receptor Information
>4ydd Chain A (length=895) Species: 640081 (Azospira oryzae PS) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ISGAFEYSGWENFHRTQWSWDKKTRGAHLVNCTGACPHFVYSKDGVVMRE
EQSKDIAPMPNIPEYNPRGCNKGECGHDYMYGPHRIKYPLIRVGERGEGK
WRRATWEEALDMIADKCVDTIKNHAPDCISVYSPVPAVSPVSFSAGHRFA
HYIGAHAHTFYDWYGDHPTGQTQTCGVQGDTCETADWFNSKYIILWGSNP
TQTRIPDAHFLSEAQLNGAKIVSISPDYNSSTIKVDKWIHPQPGTDGALA
MAMAHVIIKEKLYDAHSLKEQTDLSYLVRSDTKRFLREADVVAGGSKDKF
YFWNAKTGKPVIPKGSWGDQPEKKGSPVGFLGRNTFAFPKGYIDLGDLDP
ALEGKFNMQLLDGKTVEVRPVFEILKSRLMADNTPEKAAKITGVTAKAIT
ELAREFATAKPSMIICGGGTQHWYYSDVLLRAMHLLTALTGTEGTNGGGM
NHYIGQWKPAFVAGLVALAFPEGVNKQRFCQTTIWTYIHAEVNDEIISSD
IDTEKYLRDSITTGQMPNMPEQGRDPKVFFVYRGNWLNQAKGQKYVLENL
WPKLELIVDINIRMDSTALYSDVVLPSAHWYEKLDLNVTSEHSYINMTEP
AIKPMWESKTDWQIFLALAKRVEMAAKRKKYEKFNDEKFKWVRDLSNLWN
QMTMDGKLAEDEAAAQYILDNAPQSKGITIQMLREKPQRFKSNWTSPLKE
GVPYTPFQYFVVDKKPWPTLTGRQQFYLDHDTFFDMGVELPTYKAPIDAD
KYPFRFNSPHSRHSVHSTFKDNVLMLRLQRGGPSIEMSPLDAKPLGIKDN
DWVEAWNNHGKVICRVKIRNGEQRGRVSMWHCPELYMDLLTGGSQSVCPV
RINPTNLVGNYGHLFFRPNYYGPAGSQRDVRVNVKRYIGATPISF
Ligand information
Ligand IDMGD
InChIInChI=1S/C20H26N10O13P2S2/c21-19-26-13-7(15(33)28-19)24-6-12(47)11(46)5(41-17(6)25-13)2-40-45(37,38)43-44(35,36)39-1-4-9(31)10(32)18(42-4)30-3-23-8-14(30)27-20(22)29-16(8)34/h3-6,9-10,17-18,24,31-32,46-47H,1-2H2,(H,35,36)(H,37,38)(H3,22,27,29,34)(H4,21,25,26,28,33)/t4-,5-,6+,9-,10-,17-,18-/m1/s1
InChIKeyVQAGYJCYOLHZDH-ILXWUORBSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=NC2=C(N[CH]3[CH](N2)O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6C(=O)NC(=Nc56)N)C(=C3S)S)C(=O)N1
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(=C(C5C(O4)NC6=C(N5)C(=O)NC(=N6)N)S)S)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]4C(=C([C@H]5[C@@H](O4)NC6=C(N5)C(=O)NC(=N6)N)S)S)O)O)N=C(NC2=O)N
ACDLabs 10.04O=C1C=2NC3C(S)=C(S)C(OC3NC=2N=C(N)N1)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c5N=C(N)NC4=O)C(O)C6O
CACTVS 3.341NC1=NC2=C(N[C@@H]3[C@H](N2)O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6C(=O)NC(=Nc56)N)C(=C3S)S)C(=O)N1
FormulaC20 H26 N10 O13 P2 S2
Name2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE;
MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE
ChEMBL
DrugBank
ZINCZINC000195757106
PDB chain4ydd Chain A Residue 1003 [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)
D170 G201 N203 Q206 T207 I228 S229 P230 D231 N233 D250 G421 G422 G423 W427 I458 G459 N761 P763 H764 S765 S768 V769 H770 R830 R882
Binding residue
(residue number reindexed from 1)
D166 G197 N199 Q202 T203 I224 S225 P226 D227 N229 D246 G417 G418 G419 W423 I454 G455 N757 P759 H760 S761 S764 V765 H766 R826 R878
Annotation score4
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) K72 P134 P136 W163 Y164 D166 P168 Y453 Q456
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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