Structure of PDB 4rh0 Chain A Binding Site BS01

Receptor Information
>4rh0 Chain A (length=340) Species: 420246 (Geobacillus thermodenitrificans NG80-2) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KPFVPKLVYFEPEALSYPLGKELYEKFTQMGIKIRETTSHNQVRGIPGET
ELARYRNAKSTLVVGVRRTLKFDSCKPSAEYAIPLATGCMGHCHYCYLQT
TLGSKPYIRVYVNLDDIFAQAQKYINERAPEITRFEAAATSDIVGIDHLT
HSLKKAIEFIGATDYGRLRFVTKYEHVDHLLDARHNGKTRFRFSINSRYV
INHFEPGTSSFDGRLAAARKVAGAGYKLGFVVAPIYRHEGWERGYFELFQ
ELARQLEGMDLSDLTFELIQHRFTKPAKRVIEQRYPKTRLDLDETKRKYK
WGRYGIGKYVYRDEEAKELEDTMRRYIEQFFPGAYVQYFT
Ligand information
Ligand IDEEM
InChIInChI=1S/C15H22N6O5Se/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/p+1/t7-,8+,10+,11+,14+,27-/m0/s1
InChIKeyGGJFWMOVUFBSIN-FCKMPRQPSA-O
SMILES
SoftwareSMILES
CACTVS 3.341C[Se+](CC[CH](N)C(O)=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
CACTVS 3.341C[Se@@+](CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
OpenEye OEToolkits 1.5.0C[Se+](CCC(C(=O)O)N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
OpenEye OEToolkits 1.5.0C[Se@@+](CC[C@@H](C(=O)O)N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
ACDLabs 10.04O=C(O)C(N)CC[Se+](C)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC15 H23 N6 O5 Se
Name[(3S)-3-amino-4-hydroxy-4-oxo-butyl]-[[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl]-methyl-selanium;
Se-ADENOSYLSELENOMETHIONINE
ChEMBL
DrugBank
ZINC
PDB chain4rh0 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4rh0 Rescuing DNA repair activity by rewiring the H-atom transfer pathway in the radical SAM enzyme, spore photoproduct lyase.
Resolution2.1 Å
Binding residue
(original residue number in PDB)
Y96 Y98 A139 S142 D143 V172 K174 S195 A234 P235 H272 R273
Binding residue
(residue number reindexed from 1)
Y95 Y97 A138 S141 D142 V171 K173 S194 A233 P234 H271 R272
Annotation score1
Enzymatic activity
Enzyme Commision number 4.1.99.14: spore photoproduct lyase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0003913 DNA photolyase activity
GO:0016829 lyase activity
GO:0046872 metal ion binding
GO:0051536 iron-sulfur cluster binding
GO:0051539 4 iron, 4 sulfur cluster binding
GO:1904047 S-adenosyl-L-methionine binding
Cellular Component
GO:0042601 endospore-forming forespore

View graph for
Molecular Function

View graph for
Cellular Component
External links
PDB RCSB:4rh0, PDBe:4rh0, PDBj:4rh0
PDBsum4rh0
PubMed25285338
UniProtA4IQU1

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