Structure of PDB 1djn Chain B Binding Site BS03

Receptor Information
>1djn Chain B (length=729) Species: 2327 (Methylophilus methylotrophus W3A1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ARDPKHDILFEPIQIGPKTLRNRFYQVPHCIGAGSDKPGFQSAHRSVKAE
GGWAALNTEYCSINPESDDTHRLSARIWDEGDVRNLKAMTDEVHKYGALA
GVELWYGGAHAPNMESRATPRGPSQYASEFETLSYCKEMDLSDIAQVQQF
YVDAAKRSRDAGFDIVYVYGAHSYLPLQFLNPYYNKRTDKYGGSLENRAR
FWLETLEKVKHAVGSDCAIATRFGVDTVYGPGQIEAEVDGQKFVEMADSL
VDMWDITIGDIAEWGEDAGPSRFYQQGHTIPWVKLVKQVSKKPVLGVGRY
TDPEKMIEIVTKGYADIIGCARPSIADPFLPQKVEQGRYDDIRVCIGCNV
CISRWEIGGPPMICTQNATAGEEYRRGWHPEKFRQTKNKDSVLIVGAGPS
GSEAARVLMESGYTVHLTDTAEKIGGHLNQVAALPGLGEWSYHRDYRETQ
ITKLLKKNKESQLALGQKPMTADDVLQYGADKVIIATGARWNTDGTNCLT
HDPIPGADASLPDQLTPEQVMDGKKKIGKRVVILNADTYFMAPSLAEKLA
TAGHEVTIVSGVHLANYMHFTLEYPNMMRRLHELHVEELGDHFCSRIEPG
RMEIYNIWGDGSKRTYRGPGVSPRDANTSHRWIEFDSLVLVTGRHSECTL
WNELKARESEWAENDIKGIYLIGDAEAPRLIADATFTGHRVAREIEEANP
QIAIPYKRETIAWGTPHMPGGNFKIEYKV
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain1djn Chain B Residue 1803 [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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PDB1djn Structural and biochemical characterization of recombinant wild type and a C30A mutant of trimethylamine dehydrogenase from methylophilus methylotrophus (sp. W(3)A(1)).
Resolution2.2 Å
Binding residue
(original residue number in PDB)		V395 G396 G398 P399 S400 D419 T420 G426 H427 M470 T487 G488 D674
Binding residue
(residue number reindexed from 1)		V395 G396 G398 P399 S400 D419 T420 G426 H427 M470 T487 G488 D674
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) C30 Y169 H172 Y174 R222 Y229 D267 V350
Catalytic site (residue number reindexed from 1) C30 Y169 H172 Y174 R222 Y229 D267 V350
Enzyme Commision number 1.5.8.2: trimethylamine dehydrogenase.
Gene Ontology
Molecular Function
GO:0010181 FMN binding
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0050470 trimethylamine dehydrogenase activity
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0009056 catabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1djn, PDBe:1djn, PDBj:1djn
PDBsum1djn
PubMed10869173
UniProtP16099|DHTM_METME Trimethylamine dehydrogenase (Gene Name=tmd)

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