Home Research COVID-19 Services Publications People Teaching Job Opening News Forum Lab Only
Online Services

●I-TASSER ●I-TASSER-MTD ●C-I-TASSER ●CR-I-TASSER ●QUARK ●C-QUARK ●LOMETS ●MUSTER ●CEthreader ●SEGMER ●DeepFold ●DeepFoldRNA ●FoldDesign ●COFACTOR ●COACH ●MetaGO ●TripletGO ●IonCom ●FG-MD ●ModRefiner ●REMO ●DEMO ●DEMO-EM ●SPRING ●COTH ●Threpp ●PEPPI ●BSpred ●ANGLOR ●EDock ●BSP-SLIM ●SAXSTER ●FUpred ●ThreaDom ●ThreaDomEx ●EvoDesign ●BindProf ●BindProfX ●SSIPe ●GPCR-I-TASSER ●MAGELLAN ●ResQ ●STRUM ●DAMpred

●TM-score ●TM-align ●US-align ●MM-align ●RNA-align ●NW-align ●LS-align ●EDTSurf ●MVP ●MVP-Fit ●SPICKER ●HAAD ●PSSpred ●3DRobot ●MR-REX ●I-TASSER-MR ●SVMSEQ ●NeBcon ●ResPRE ●TripletRes ●DeepPotential ●WDL-RF ●ATPbind ●DockRMSD ●DeepMSA ●FASPR ●EM-Refiner ●GPU-I-TASSER

●BioLiP ●E. coli ●GLASS ●GPCR-HGmod ●GPCR-RD ●GPCR-EXP ●Tara-3D ●TM-fold ●DECOYS ●POTENTIAL ●RW/RWplus ●EvoEF ●HPSF ●THE-DB ●ADDRESS ●Alpaca-Antibody ●CASP7 ●CASP8 ●CASP9 ●CASP10 ●CASP11 ●CASP12 ●CASP13 ●CASP14

BioLiP

Structure of PDB 1djq Chain B Binding Site BS02

Receptor Information
>1djq 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]
ARDPKHDILFEPIQIGPKTLRNRFYQVPHAIGAGSDKPGFQSAHRSVKAE
GGWAALNTEYCSINPESDDTHRLSARIWDEGDVRNLKAMTDEVHKYGALA
GVELWYGGAHAPNMESRATPRGPSQYASEFETLSYCKEMDLSDIAQVQQF
YVDAAKRSRDAGFDIVYVYGAHSYLPLQFLNPYYNKRTDKYGGSLENRAR
FWLETLEKVKHAVGSDCAIATRFGVDTVYGPGQIEAEVDGQKFVEMADSL
VDMWDITIGDIAEWGEDAGPSRFYQQGHTIPWVKLVKQVSKKPVLGVGRY
TDPEKMIEIVTKGYADIIGCARPSIADPFLPQKVEQGRYDDIRVCIGCNV
CISRWEIGGPPMICTQNATAGEEYRRGWHPEKFRQTKNKDSVLIVGAGPS
GSEAARVLMESGYTVHLTDTAEKIGGHLNQVAALPGLGEWSYHRDYRETQ
ITKLLKKNKESQLALGQKPMTADDVLQYGADKVIIATGARWNTDGTNCLT
HDPIPGADASLPDQLTPEQVMDGKKKIGKRVVILNADTYFMAPSLAEKLA
TAGHEVTIVSGVHLANYMHFTLEYPNMMRRLHELHVEELGDHFCSRIEPG
RMEIYNIWGDGSKRTYRGPGVSPRDANTSHRWIEFDSLVLVTGRHSECTL
WNELKARESEWAENDIKGIYLIGDAEAPRLIADATFTGHRVAREIEEANP
QIAIPYKRETIAWGTPHMPGGNFKIEYKV
Ligand information
Ligand IDFMN
InChIInChI=1S/C17H21N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29/h3-4,11-12,14,22-24H,5-6H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11-,12+,14-/m0/s1
InChIKeyFVTCRASFADXXNN-SCRDCRAPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)O)O)O)O
OpenEye OEToolkits 1.7.6Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O
ACDLabs 12.01N=2C(=O)NC(=O)C3=Nc1cc(C)c(C)cc1N(C=23)CC(O)C(O)C(O)COP(=O)(O)O
CACTVS 3.385Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O)c2cc1C
CACTVS 3.385Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O)c2cc1C
FormulaC17 H21 N4 O9 P
NameFLAVIN MONONUCLEOTIDE;
RIBOFLAVIN MONOPHOSPHATE
ChEMBLCHEMBL1201794
DrugBankDB03247
ZINCZINC000003831425
PDB chain1djq Chain B Residue 1802 [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]
PDB1djq 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)		P28 H29 A30 E59 Y60 E103 Y169 R222 W264 D267 A268 V297 R299 C320 A321 R322 P323 I352
Binding residue
(residue number reindexed from 1)		P28 H29 A30 E59 Y60 E103 Y169 R222 W264 D267 A268 V297 R299 C320 A321 R322 P323 I352
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) A30 Y169 H172 Y174 R222 Y229 D267 V350
Catalytic site (residue number reindexed from 1) A30 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:1djq, PDBe:1djq, PDBj:1djq
PDBsum1djq
PubMed10869173
UniProtP16099|DHTM_METME Trimethylamine dehydrogenase (Gene Name=tmd)

[Back to BioLiP]

zhanglabzhanggroup.org | +65-6601-1241 | Computing 1, 13 Computing Drive, Singapore 117417