Structure of PDB 4cvn Chain D Binding Site BS01

Receptor Information
>4cvn Chain D (length=165) Species: 272844 (Pyrococcus abyssi GE5) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLIAITGTPGVGKTTIAKLLAEKLGYEYVNLRDFALEKGEVEIDELAYFV
ERNVVLDGHLSHLMPVDLVVVLRAHPRIIGERLRERGYSKEKIGENVEAE
LVDAILIEAIDEHENVIEVDTTNKTPEEIVEEIIGLIKSGVKRRVGIVDW
SEVYDEIIPYLRLGG
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain4cvn Chain D Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4cvn RNA Mimicry by the Fap7 Adenylate Kinase in Ribosome Biogenesis
Resolution2.121 Å
Binding residue
(original residue number in PDB)		G10 V11 G12 K13 T14 T15 R96 R100 K138 P140
Binding residue
(residue number reindexed from 1)		G10 V11 G12 K13 T14 T15 R82 R86 K124 P126
Annotation score5
Enzymatic activity
Enzyme Commision number 2.7.4.3: adenylate kinase.
Gene Ontology
Molecular Function
GO:0004017 adenylate kinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016887 ATP hydrolysis activity
Biological Process
GO:0006364 rRNA processing
GO:0016310 phosphorylation
GO:0042254 ribosome biogenesis
GO:0042274 ribosomal small subunit biogenesis
GO:0046940 nucleoside monophosphate phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4cvn, PDBe:4cvn, PDBj:4cvn
PDBsum4cvn
PubMed24823650
UniProtQ9UZK4|KAD6_PYRAB Putative adenylate kinase (Gene Name=PYRAB11420)

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