Structure of PDB 1zip Chain A Binding Site BS02
Receptor Information
>1zip Chain A (length=217) Species:
1422
(Geobacillus stearothermophilus) [
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MNLVLMGLPGAGKGTQAEKIVAAYGIPHISTGDMFRAAMKEGTPLGLQAK
QYMDRGDLVPDEVTIGIVRERLSKDDCQNGFLLDGFPRTVAQAEALETML
ADIGRKLDYVIHIDVRQDVLMERLTGRRICRNCGATYHLIFHPPAKPGVC
DKCGGELYQRADDNEATVANRLEVNMKQMKPLVDFYEQKGYLRNINGEQD
MEKVFADIRELLGGLAR
Ligand information
Ligand ID
AP5
InChI
InChI=1S/C20H29N10O22P5/c21-15-9-17(25-3-23-15)29(5-27-9)19-13(33)11(31)7(47-19)1-45-53(35,36)49-55(39,40)51-57(43,44)52-56(41,42)50-54(37,38)46-2-8-12(32)14(34)20(48-8)30-6-28-10-16(22)24-4-26-18(10)30/h3-8,11-14,19-20,31-34H,1-2H2,(H,35,36)(H,37,38)(H,39,40)(H,41,42)(H,43,44)(H2,21,23,25)(H2,22,24,26)/t7-,8-,11-,12-,13-,14-,19-,20-/m1/s1
InChIKey
OIMACDRJUANHTJ-XPWFQUROSA-N
SMILES
Software
SMILES
OpenEye OEToolkits 1.5.0
c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)N
CACTVS 3.341
Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P@](O)(=O)O[P@](O)(=O)O[P@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0
c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)N
CACTVS 3.341
Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)[CH](O)[CH]3O
Formula
C20 H29 N10 O22 P5
Name
BIS(ADENOSINE)-5'-PENTAPHOSPHATE
ChEMBL
CHEMBL437508
DrugBank
DB01717
ZINC
ZINC000096085195
PDB chain
1zip Chain A Residue 218 [
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Receptor-Ligand Complex Structure
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PDB
1zip
Crystal structures of Bacillus stearothermophilus adenylate kinase with bound Ap5A, Mg2+ Ap5A, and Mn2+ Ap5A reveal an intermediate lid position and six coordinate octahedral geometry for bound Mg2+ and Mn2+.
Resolution
1.85 Å
Binding residue
(original residue number in PDB)
P9 G10 G12 K13 G14 T15 T31 G32 F35 R36 M53 D57 L58 V59 T64 R88 Q92 R123 R127 F141 R160 R171 M201
Binding residue
(residue number reindexed from 1)
P9 G10 G12 K13 G14 T15 T31 G32 F35 R36 M53 D57 L58 V59 T64 R88 Q92 R123 R127 F141 R160 R171 M201
Annotation score
4
Enzymatic activity
Catalytic site (original residue number in PDB)
K13 R88 R127 R160 R171
Catalytic site (residue number reindexed from 1)
K13 R88 R127 R160 R171
Enzyme Commision number
2.7.4.3
: adenylate kinase.
Gene Ontology
Molecular Function
GO:0004017
adenylate kinase activity
GO:0004550
nucleoside diphosphate kinase activity
GO:0005524
ATP binding
GO:0008270
zinc ion binding
GO:0016301
kinase activity
GO:0016776
phosphotransferase activity, phosphate group as acceptor
GO:0019205
nucleobase-containing compound kinase activity
GO:0046872
metal ion binding
GO:0050145
nucleoside monophosphate kinase activity
Biological Process
GO:0006139
nucleobase-containing compound metabolic process
GO:0009123
nucleoside monophosphate metabolic process
GO:0009132
nucleoside diphosphate metabolic process
GO:0009165
nucleotide biosynthetic process
GO:0016310
phosphorylation
GO:0044209
AMP salvage
GO:0046940
nucleoside monophosphate phosphorylation
Cellular Component
GO:0005737
cytoplasm
GO:0005829
cytosol
View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB
RCSB:1zip
,
PDBe:1zip
,
PDBj:1zip
PDBsum
1zip
PubMed
9715904
UniProt
P27142
|KAD_GEOSE Adenylate kinase (Gene Name=adk)
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