Structure of PDB 5gz5 Chain A Binding Site BS04

Receptor Information
>5gz5 Chain A (length=777) Species: 8656 (Naja atra) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YQDICVLPTQSWSCNKLRCGEKRMANVLCSCSEDCLTKKDCCTDYKSICK
RETSWLKDQCASQCPEGFDQSPLILFSMDGFRAEYLETWDTLMPNINKLK
TCGTHAKYMRAVYPTKTFVNHYTIVTGLYAETHGIIDNNMYDVKLNQNFS
LSGSNMRNAAWWGGQPIWHTASYQGLKAATYFWPGSEVKINGSYPTIYKV
YNKSTPFEARVMEVLKWLDLPKAKRPDFSTLYIEEPDTTGHKFGPVSGQV
IKSLQMADRTLGMLMEGLKQRNLHNCVNLILLADHGMEAISCNRLEYMTD
YFNTVDFFMYEGAAPRIRSKNVPKDFYTFDSEAIVKKLTCRKPKQHFKAY
LAKDLPKRLHFANNIRIDKVNLMVDRQWLAVRNKKYKYCSGGTHGYDNEF
KSMEAIFLAHGPGFKEKTEVTSFENIEVYNLMCDLLKLKPAPNNGTHGSL
NHLLKNPFYNPSPAKEQSPPLYCLFGPVPSPDVSGCKCSSITDLEAVNQR
LNLIDQAKMQSEADNLPYGRPHVLQHSKYCLLHQTKYISAYSQDILMPLW
NSYTISKSLPSASDCLRLDVRIPTVQSQTCSNYQPDLAITPGFLYPPDFS
SSGPEQYDALITSNIVPMYKEFARLWNYFHSTLLPKYATERNGLNVISGP
IFDYNYDGHFDPYDTIDQYVNNTKIPIPTHYFVVLTSCENSTKTPLNCPP
GSLKVLSFILPHRPDNSESCADKSPDNLWVEERMQTHTARVRDVELLTGL
DFYSALKQPLSETLRLKTFLPIFINSV
Ligand information
Ligand IDAMP
InChIInChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyUDMBCSSLTHHNCD-KQYNXXCUSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
ACDLabs 12.01O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
FormulaC10 H14 N5 O7 P
NameADENOSINE MONOPHOSPHATE
ChEMBLCHEMBL752
DrugBankDB00131
ZINCZINC000003860156
PDB chain5gz5 Chain A Residue 1016 [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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PDB5gz5 Crystal structure of snake venom phosphodiesterase (PDE) from Taiwan cobra (Naja atra atra) in complex with AMP
Resolution2.093 Å
Binding residue
(original residue number in PDB)		T185 F186 Y269 K271 Y300 D305 H309 H462
Binding residue
(residue number reindexed from 1)		T117 F118 Y201 K203 Y232 D237 H241 H394
Annotation score5
Enzymatic activity
Enzyme Commision number 3.6.1.-
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0016787 hydrolase activity
GO:0043262 ADP phosphatase activity
GO:0046872 metal ion binding
GO:0047429 nucleoside triphosphate diphosphatase activity
GO:0090729 toxin activity
Biological Process
GO:0009143 nucleoside triphosphate catabolic process
GO:0035821 modulation of process of another organism
Cellular Component
GO:0005576 extracellular region

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5gz5, PDBe:5gz5, PDBj:5gz5
PDBsum5gz5
PubMed
UniProtA0A2D0TC04|PDE_NAJAT Venom phosphodiesterase

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