Structure of PDB 2zxh Chain B Binding Site BS01

Receptor Information
>2zxh Chain B (length=601) Species: 63363 (Aquifex aeolicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DEFDVVVIGGGHAGIEAALAAARMGAKTAMFVLNADTIGQMSCNPAIGGI
AKGIVVREIDALGGEMGKAIDQTGIQFKMLNTRKGKAVQSPRAQADKKRY
REYMKKVCENQENLYIKQEEVVDIIVKNNQVVGVRTNLGVEYKTKAVVVT
TGTFLNGVIYIGDKMIPGGRLGEPRSEGLSDFYRRFDFPLIRFKTGTPAR
LDKRTIDFSALEVAPGDDPPPKFSFWTEPVGSYWFPKGKEQVNCWITYTT
PKTHEIIRKNLHRTALYGGLIKGIGPRYCPSIEDKIVKFPDKERHQIFLE
PEGLDTIEIYPNGLSTSLPEEVQWEMYRSIPGLENVVLIRPAYAIEYDVV
PPTELYPTLETKKIRGLFHAGNFNGTTGYEEAAGQGIVAGINAALRAFGK
EPIYLRRDESYIGVMIDDLTTKGVTEPYRLFTSRSEYRLYIRQDNAILRL
AKLGRELGLLSEEQYKLVKELEREIEKWKEFYKSERVRSYSVATLMTMNY
TLDDVKEKFGYEVPQHPYVKEEVEIQLKYEPYIERERKLNEKLKKLEDTK
IPPDIDYDKIPGLTKEAREKLKKFKPITVGQASRIDGITPAAITALLVYL
G
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 chain2zxh Chain B Residue 618 [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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PDB2zxh Conserved cysteine residues of GidA are essential for biogenesis of 5-carboxymethylaminomethyluridine at tRNA anticodon
Resolution3.2 Å
Binding residue
(original residue number in PDB)		I13 G14 G15 G16 H17 A18 L38 C48 V126 T156 G157 F159 S181 T200 G201 Y348 I350 N377 T382 G383 A387
Binding residue
(residue number reindexed from 1)		I8 G9 G10 G11 H12 A13 L33 C43 V121 T151 G152 F154 S176 T195 G196 Y343 I345 N372 T377 G378 A382
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:2zxh, PDBe:2zxh, PDBj:2zxh
PDBsum2zxh
PubMed19446527
UniProtO66962|MNMG_AQUAE tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG (Gene Name=mnmG)

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