Structure of PDB 7mdi Chain C Binding Site BS01

Receptor Information
>7mdi Chain C (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 D Residue 804 [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)		S251 C294
Binding residue
(residue number reindexed from 1)		S247 C290
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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