Structure of PDB 5m1d Chain A Binding Site BS02

Receptor Information
>5m1d Chain A (length=469) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YNDLRDFLTLLEQQGELKRITLPVDPHLEITEIADRTLRAGGPALLFENP
KGYSMPVLCNLFGTPKRVAMGMGQEDVSALREVGKLLAFLKKQVLNMPTK
RLRGAPCQQKIVSGDDVDLNRIPIMTCWPEDAAPLITWGLTVTRGPHKER
QNLGIYRQQLIGKNKLIMRWLSHRGGALDYQEWCAAHPGERFPVSVALGA
DPATILGAVTPVPDTLSEYAFAGLLRGTKTEVVKCISNDLEVPASAEIVL
EGYIEQGETAPEGPYGDHTGYYNEVDSFPVFTVTHITQREDAIYHSTYTG
RPPDEPAVLGVALNEVFVPILQKQFPEIVDFYLPPEGCSYRLAVVTIKKQ
YAGHAKRVMMGVWSFLRQFMYTKFVIVCDDDVNARDWNDVIWAITTRMDP
ARDTVLVENTPIDYLDFASPVSGLGSKMGLDATNKWPGETQREWGRPIKK
DPDVVAHIDAIWDELAIFN
Ligand information
Ligand ID4LU
InChIInChI=1S/C22H29N4O9P/c1-10-7-12-16-15(11(10)2)22(3,4)5-6-25(16)17-19(23-21(31)24-20(17)30)26(12)8-13(27)18(29)14(28)9-35-36(32,33)34/h6-7,13-14,18,27-29H,5,8-9H2,1-4H3,(H3-,23,24,30,31,32,33,34)/p+1/t13-,14+,18-/m0/s1
InChIKeyKOUJZPGFPGLHCZ-IYOUNJFTSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2Cc1cc2c3c(c1C)C(CC=[N+]3C4=C(N2C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O)NC(=O)NC4=O)(C)C
CACTVS 3.385Cc1cc2N(C[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O)C3=C(C(=O)NC(=O)N3)[N+]4=CCC(C)(C)c(c1C)c24
OpenEye OEToolkits 1.9.2Cc1cc2c3c(c1C)C(CC=[N+]3C4=C(N2CC(C(C(COP(=O)(O)O)O)O)O)NC(=O)NC4=O)(C)C
CACTVS 3.385Cc1cc2N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O)C3=C(C(=O)NC(=O)N3)[N+]4=CCC(C)(C)c(c1C)c24
ACDLabs 12.01c1c3c4c(c(c1C)C)C(C)(CC=[N+]4C2=C(NC(NC2=O)=O)N3CC(C(C(O)COP(O)(O)=O)O)O)C
FormulaC22 H30 N4 O9 P
Name1-deoxy-5-O-phosphono-1-(3,3,4,5-tetramethyl-9,11-dioxo-2,3,8,9,10,11-hexahydro-7H-quinolino[1,8-fg]pteridin-12-ium-7-y l)-D-ribitol;
prenylated-FMN iminium form
ChEMBL
DrugBank
ZINCZINC000263614449
PDB chain5m1d Chain A Residue 502 [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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PDB5m1d Oxidative Maturation and Structural Characterization of Prenylated FMN Binding by UbiD, a Decarboxylase Involved in Bacterial Ubiquinone Biosynthesis.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		T160 N175 I178 R180 R192 L194 R197 V232
Binding residue
(residue number reindexed from 1)		T137 N152 I155 R157 R169 L171 R174 V209
Annotation score1
Enzymatic activity
Enzyme Commision number 4.1.1.98: 4-hydroxy-3-polyprenylbenzoate decarboxylase.
Gene Ontology
Molecular Function
GO:0008694 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity
GO:0016831 carboxy-lyase activity
GO:0030145 manganese ion binding
GO:0042802 identical protein binding
GO:0046872 metal ion binding
GO:0120233 prenyl-FMNH2 binding
Biological Process
GO:0006744 ubiquinone biosynthetic process
GO:0032150 ubiquinone biosynthetic process from chorismate
GO:0034214 protein hexamerization
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5m1d, PDBe:5m1d, PDBj:5m1d
PDBsum5m1d
PubMed28057757
UniProtP0AAB4|UBID_ECOLI 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (Gene Name=ubiD)

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