Structure of PDB 6ybp Chain F Binding Site BS02

Receptor Information
>6ybp Chain F (length=506) Species: 272630 (Methylorubrum extorquens AM1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LEKLEERRAQARLGGGEKRLEAQHKRGKLTARERIELLLDHGSFEEFDMF
VQHRSTDFGMEKQKIPGDGVVTGWGTVNGRTVFLFSKDFTVFGGSLSEAH
AAKIVKVQDMALKMRAPIIGIFDAGGARIQEGVAALGGYGEVFRRNVAAS
GVIPQISVIMGPCAGGDVYSPAMTDFIFMVRDTSYMFVTGPDVVKTVTNE
VVTAEELGGAKVHTSKSSIADGSFENDVEAILQIRRLLDFLPANNIEGVP
EIESFDDVNRLDKSLDTLIPDNPNKPYDMGELIRRVVDEGDFFEIQAAYA
RNIITGFGRVEGRTVGFVANQPLVLAGVLDSDASRKAARFVRFCNAFSIP
IVTFVDVPGFLPGTAQEYGGLIKHGAKLLFAYSQATVPLVTIITRKAFGG
AYDVMASKHVGADLNYAWPTAQIAVMGAKGAVEIIFRAEIGDADKIAERT
KEYEDRFLSPFVAAERGYIDEVIMPHSTRKRIARALGMLRTKEMEQPWKK
HDNIPL
Ligand information
Ligand IDBTI
InChIInChI=1S/C10H16N2O2S/c13-5-3-1-2-4-8-9-7(6-15-8)11-10(14)12-9/h5,7-9H,1-4,6H2,(H2,11,12,14)/t7-,8-,9-/m0/s1
InChIKeyARDNWGMSCXSPBF-CIUDSAMLSA-N
SMILES
SoftwareSMILES
CACTVS 3.341O=CCCCC[CH]1SC[CH]2NC(=O)N[CH]12
CACTVS 3.341O=CCCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12
OpenEye OEToolkits 1.5.0C1[C@H]2[C@@H]([C@@H](S1)CCCCC=O)NC(=O)N2
ACDLabs 10.04O=C1NC2C(SCC2N1)CCCCC=O
OpenEye OEToolkits 1.5.0C1C2C(C(S1)CCCCC=O)NC(=O)N2
FormulaC10 H16 N2 O2 S
Name5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL
ChEMBL
DrugBankDB07497
ZINCZINC000036470912
PDB chain6ybp Chain K Residue 701 [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]
PDB6ybp A new-to-nature carboxylation module to improve natural and synthetic CO2 fixation
Resolution3.48 Å
Binding residue
(original residue number in PDB)		F364 P366
Binding residue
(residue number reindexed from 1)		F360 P362
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) G169 G170 G404 A405
Catalytic site (residue number reindexed from 1) G165 G166 G400 A401
Enzyme Commision number 6.4.1.3: propionyl-CoA carboxylase.
Gene Ontology
Molecular Function
GO:0004658 propionyl-CoA carboxylase activity
GO:0016874 ligase activity

View graph for
Molecular Function
External links
PDB RCSB:6ybp, PDBe:6ybp, PDBj:6ybp
PDBsum6ybp
PubMed
UniProtC5AP75

[Back to BioLiP]