Structure of PDB 3cp8 Chain C Binding Site BS01

Receptor Information
>3cp8 Chain C (length=611) Species: 194439 (Chlorobaculum tepidum TLS) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMYDVIVVGAGHAGCEAALAVARGGLHCLLITSDLSAVARMSCNPAIGGV
AKGQITREIDALGGEMGKAIDATGIQFRMLNRSKGPAMHSPRAQADKTQY
SLYMRRIVEHEPNIDLLQDTVIGVSANSGKFSSVTVRSGRAIQAKAAILA
CGTFLNGLIHIGMDHFPGGRSTAEPPVEGLTESLASLGFSFGRLKTGTPP
RIDSRSVDYTIVTEQPGDVDPVPFSFSSTSVANRNLVSCYLTKTTEKTHD
ILRTGFDRSPLFTGCPSIEDKISRFPDKSSHHIFLEPEGTDTVEMYVNGF
STSLPEDIQIAGLRSIPGLEEAKMIRPGYAIEYDFFHPWQIRSTMETRPV
ENLFFAGQINGTSGYEEAAAQGLMAGINAVRKILGKELIVLGRDQAYIGV
LIDDLITKETKEPYRMFTSSAEHRLILRHDNADLRLRKIGYDCNLVSSDD
LHRTESIIKRVQHCLEVMKTAKVTPAEINTLLMNKGLQELKTPARALSLI
KRPGISLQDILEHSLSVRSAAEELCNDPRVAEQVQIEIKYEGYIKREQLV
ADRIARLDSLHIPDNFNYDSLNSLSSEGREKLLKHRPATIGQASRILGVS
PSDVSILMIRL
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 chain3cp8 Chain C Residue 622 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3cp8 Crystal structures of the conserved tRNA-modifying enzyme GidA: implications for its interaction with MnmE and substrate
Resolution3.2 Å
Binding residue
(original residue number in PDB)		G8 G10 H11 T31 S32 C42 K51 T119 V120 C150 G151 F153 V176 T195 G196 G365 Q366 G372 Y373 E374 A376
Binding residue
(residue number reindexed from 1)		G9 G11 H12 T32 S33 C43 K52 T120 V121 C151 G152 F154 V177 T196 G197 G357 Q358 G364 Y365 E366 A368
Annotation score4
Enzymatic activity
Enzyme Commision number 1.-.-.-
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3cp8, PDBe:3cp8, PDBj:3cp8
PDBsum3cp8
PubMed18565343
UniProtQ8KA85|MNMG_CHLTE tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG (Gene Name=mnmG)

[Back to BioLiP]