Structure of PDB 5im3 Chain A Binding Site BS04

Receptor Information
>5im3 Chain A (length=874) Species: 208964 (Pseudomonas aeruginosa PAO1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LRVIKRNGTVVPYTDDKITVAITKAFLAVEGGTAAASSRIHDTVRRLTEQ
VTATFKRRMPSGGTIHIEEIQDQVELALMRAGEQKVARDYVIYREARAAE
RKNAGAASDVAQPHPSIRITRADGSLSPLDMGRLNTIISEACEGLAEVDG
ALIERETLKNLYDGVAEKDVNTALVMTARTLVEREPNYSYVTARLLMDTL
RAEALGFLGVAESATHHEMAELYAKALPAYIEKGAEFELVDAKLKEFDLE
KLGKAIDHERDQQFTYLGLQTLYDRYFIHKDGIRFELPQIFFMRVAMGLA
IEEKDREARAIEFYNLLSSFDYMSSTPTLFNAGTLRPQLSSCYLTTVPDD
LSGIYGAIHDNAMLSKFAGGLGNDWTPVRALGSYIKGTNGKSQGVVPFLK
VVNDTAVAVNAVCAYLETWHLDIEEFLELRKNTGDDRRRTHDMNTANWIP
DLFMKRVFDDGSWTLFSPSDVPDLHDLYGKAFEERYEYYEALASYGKLKL
HKVVQAKDLWRKMLSMLFETGHPWLTFKDPCNLRSPQQHVGVVHSSNLCT
EITLNTNKDEIAVCNLGSINLVNHIVDGKLDTAKLEKTVKTAVRMLDNVI
DINYYSVPQAQNSNFKHRPVGLGIMGFQDALYLQHIPYGSDAAIAFADQS
MEAISYYAIQASCDLADERGAYQTFQGSLWSQGILPIDSEKKLIEERGAK
YIEVDLSETLDWAPLRERVQKGIRNSNIMAIAPTATIANITGVSQSIEPT
YQNLYVKSNLSGEFTVINPYLVRDLKARGLWDPVMVNDLKYYDGSVQQIE
RIPQDLKDLYATAFEVETRWIVEAASRRQKWIDQAQSLNLYIAGASGKKL
DVTYRMAWFRGLKTTYYLRALAAT
Ligand information
Ligand IDDTP
InChIInChI=1S/C10H16N5O12P3/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(25-7)2-24-29(20,21)27-30(22,23)26-28(17,18)19/h3-7,16H,1-2H2,(H,20,21)(H,22,23)(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1
InChIKeySUYVUBYJARFZHO-RRKCRQDMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O3
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O
FormulaC10 H16 N5 O12 P3
Name2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
ChEMBLCHEMBL335538
DrugBankDB03222
ZINCZINC000008215662
PDB chain5im3 Chain A Residue 1005 [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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PDB5im3 Structural Mechanism of Allosteric Activity Regulation in a Ribonucleotide Reductase with Double ATP Cones.
Resolution2.298 Å
Binding residue
(original residue number in PDB)		D380 D381 L382 I385 R410 I416
Binding residue
(residue number reindexed from 1)		D349 D350 L351 I354 R379 I385
Annotation score1
Binding affinityMOAD: Kd~1.5uM
PDBbind-CN: -logKd/Ki=5.82,Kd~1.5uM
Enzymatic activity
Catalytic site (original residue number in PDB) C373 N585 C587 E589 C602 Y904 Y905
Catalytic site (residue number reindexed from 1) C342 N547 C549 E551 C564 Y866 Y867
Enzyme Commision number 1.17.4.1: ribonucleoside-diphosphate reductase.
Gene Ontology
Molecular Function
GO:0004748 ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
GO:0005524 ATP binding
GO:0016491 oxidoreductase activity
Biological Process
GO:0009263 deoxyribonucleotide biosynthetic process
Cellular Component
GO:0005971 ribonucleoside-diphosphate reductase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5im3, PDBe:5im3, PDBj:5im3
PDBsum5im3
PubMed27133024
UniProtQ9I4I1

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