Structure of PDB 5im3 Chain B Binding Site BS04

Receptor Information
>5im3 Chain B (length=860) Species: 208964 (Pseudomonas aeruginosa PAO1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GQLRVIKRNGTVVPYTDDKITVAITKAFLAVEAAASSRIHDTVRRLTEQV
TATFKRRMPSGGTIHIEEIQDQVELALMRAGEQKVARDYVIYREARAAER
KNASIRITRADGSLSPLDMGRLNTIISEACEGLAEVDGALIERETLKNLY
DGVAEKDVNTALVMTARTLVEREPNYSYVTARLLMDTLRAEALGFLGVAE
SATHHEMAELYAKALPAYIEKGAEFELVDAKLKEFDLEKLGKAIDHERDQ
QFTYLGLQTLYDRYFIHKDGIRFELPQIFFMRVAMGLAIEEKDREARAIE
FYNLLSSFDYMSSTPTLFNAGTLRPQLSSCYLTTVPDDLSGIYGAIHDNA
MLSKFAGGLGNDWTPVRALGSYIKGTNGKSQGVVPFLKVVNDTAVAVNAV
CAYLETWHLDIEEFLELRKNTGDDRRRTHDMNTANWIPDLFMKRVFDDGS
WTLFSPSDVPDLHDLYGKAFEERYEYYEALASYGKLKLHKVVQAKDLWRK
MLSMLFETGHPWLTFKDPCNLRSPQQHVGVVHSSNLCTEITLNTNKDEIA
VCNLGSINLVNHIVDGKLDTAKLEKTVKTAVRMLDNVIDINYYSVPQAQN
SNFKHRPVGLGIMGFQDALYLQHIPYGSDAAIAFADQSMEAISYYAIQAS
CDLADERGAYQTFQGSLWSQGILPIDSEKKLIEERGAKYIEVDLSETLDW
APLRERVQKGIRNSNIMAIAPTATIANITGVSQSIEPTYQNLYVKSNLSG
EFTVINPYLVRDLKARGLWDPVMVNDLKYYDGSVQQIERIPQDLKDLYAT
AFEVETRWIVEAASRRQKWIDQAQSLNLYIAGASGKKLDVTYRMAWFRGL
KTTYYLRALA
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 B Residue 1002 [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)		A52 K55 A56 D120 Y121 Y124 R128 R132
Binding residue
(residue number reindexed from 1)		A23 K26 A27 D88 Y89 Y92 R96 R100
Annotation score1
Binding affinityMOAD: 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) C330 N535 C537 E539 C552 Y854 Y855
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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