Structure of PDB 7mdi Chain A Binding Site BS02

Receptor Information
>7mdi Chain A (length=734) Species: 242231 (Neisseria gonorrhoeae FA 1090) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TDLKVTKRDGRLEAIDLDKIHRVVTWAAEGLENVSVSQVELKSHIQFYNG
IRTDDIHETIIKAAADLISEDTPDYQYLAARLAIFHLRKIAYGEYEPPHL
YNHVKKLTDAGKYDRHILEDYSREEFDELNAYIDHERDMSFSYAAVKQLE
GKYLVQNRVTRQIYETPQFLYVLVAMCLFSKYPKEARLDYVKRFYDAVST
FKVSLPTPIMSGVRTPTRQFSSCVLIECDDSLDSINATTSAIVKYVSQRA
GIGINAGRIRGLDSEIRGGEARHTGCIPFFKMFQAAVKSCSQGGVRGGAA
TLFYPLWHIEAESLLVLKNNRGVEDNRIRQLDYGVQINRLLYTRLIKGGN
ITLFSPNEVSGLYEAFFADQDEFERLYTKYEQDPNIRKRIIPAADLFSTL
MQERAGTGRIYIQNVDHCNTHSPFDPRVAPVHQSNLCMEIALPTKPLDNI
NDPDGEIALCTLSAFNLGALNSLDELEGLADLTVRALDALLDYQGYPVEA
ARTSTMDRRSLGIGVINYAYYLAKNGVRYSDGSALGLTHRTFEAIQYYLL
KASANLAKEYGACTLFNQTVYSQGKLPIDTYKKDLDAVCGEPLHYDWESL
RADIVKYGLRNSTLTALMPSETSSQIANATNGIEPPRGLVTVKASKDGIL
KQVVPEFETLKNAYETLWQLPGNEGYLKLVGVMQKFVDQAISANTAYDPG
KFEGNKVSMKQMLKDLLTAYKYGVKTLYYHNTRD
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 chain7mdi Chain A Residue 802 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7mdi Effects of chameleon dispense-to-plunge speed on particle concentration, complex formation, and final resolution: A case study using the Neisseria gonorrhoeae ribonucleotide reductase inactive complex.
Resolution4.3 Å
Binding residue
(original residue number in PDB)		K11 R12 D20 T57 H61
Binding residue
(residue number reindexed from 1)		K7 R8 D16 T53 H57
Annotation score1
Enzymatic activity
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:7mdi, PDBe:7mdi, PDBj:7mdi
PDBsum7mdi
PubMed34906669
UniProtQ5F8Z6

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