Structure of PDB 2zxi Chain D Binding Site BS01

Receptor Information
>2zxi Chain D (length=603) Species: 63363 (Aquifex aeolicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SHMAWVVDEFDVVVIGGGHAGIEAALAAARMGAKTAMFVLNADTIGQMSC
NPAIGGIAKGIVVREIDALGGEMGKAIDQTGIQFKMLNTRKGKAVQSPRA
QADKKRYREYMKKVCENQENLYIKQEEVVDIIVKNNQVVGVRTNLGVEYK
TKAVVVTTGTFLNGVIYIGDKMIPGGRLGEPRSEGLSDFYRRFDFPLIRF
KTGTPARLDKRTIDFSALEVAPGDDPPPKFSFWTEPVGSYWFPKGKEQVN
CWITYTTPKTHEIIRKNLHRYCPSIEDKIVKFPDKERHQIFLEPEGLDTI
EIYPNGLSTSLPEEVQWEMYRSIPGLENVVLIRPAYAIEYDVVPPTELYP
TLETKKIRGLFHAGNFNGTTGYEEAAGQGIVAGINAALRAFGKEPIYLRR
DESYIGVMIDDLTTKGVTEPYRLFTSRSEYRLYIRQDNAILRLAKLGREL
GLLSEEQYKLVKELEREIEKWKEFYKSERVSVAVGGDTRSYSVATLMTMN
YTLDDVKEKFGYEVPQHPYVKEEVEIQLKYEPYIERERKLNEKLKKLEDT
KIPPDIDYDKIPGLTKEAREKLKKFKPITVGQASRIDGITPAAITALLVY
LGK
Ligand information
Ligand IDFAD
InChIInChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
ACDLabs 10.04O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain2zxi Chain D Residue 618 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2zxi Conserved cysteine residues of GidA are essential for biogenesis of 5-carboxymethylaminomethyluridine at tRNA anticodon
Resolution2.3 Å
Binding residue
(original residue number in PDB)		I13 G14 G15 G16 A18 V37 L38 C48 E125 V126 T155 T156 G157 F159 S181 T200 G201 Y348 I350 G376 N377 T382 G383 R434
Binding residue
(residue number reindexed from 1)		I15 G16 G17 G18 A20 V39 L40 C50 E127 V128 T157 T158 G159 F161 S183 T202 G203 Y336 I338 G364 N365 T370 G371 R422
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0050660 flavin adenine dinucleotide binding
Biological Process
GO:0002098 tRNA wobble uridine modification
GO:0008033 tRNA processing
GO:0030488 tRNA methylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2zxi, PDBe:2zxi, PDBj:2zxi
PDBsum2zxi
PubMed19446527
UniProtO66962|MNMG_AQUAE tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG (Gene Name=mnmG)

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