Structure of PDB 6ybq Chain F Binding Site BS01

Receptor Information

>6ybq Chain F (length=506) Species: 272630 (Methylorubrum extorquens AM1)

LEKLEERRAQARLGGGEKRLEAQHKRGKLTARERIELLLDHGSFEEFDMF
VQHRSTDFGMEKQKIPGDGVVTGWGTVNGRTVFLFSKDFTVFGGSSSEAH
AAKIVKVQDMALKMRAPIIGIFDAGGARIQEGVAALGGHGEVFRRNVAAS
GVIPQISVIMGPCAGGDVYSPAMTDFIFMVRDTSYMFVTGPDVVKTVTNE
VVTAEELGGAKVHTSKSSIADGSFENDVEAILQIRRLLDFLPANNIEGVP
EIESFDDVNRLDKSLDTLIPDNPNKPYDMGELIRRVVDEGDFFEIQAAYA
RNIITGFGRVEGRTVGFVANQPLVLAGVLDSDASRKAARFVRFCNAFSIP
IVTFVDVPGFLPGTAQEYGGLIKHGAKLLFAYSQATVPLVTIITRKAFGG
AYIVMASKHVGADLNYAWPTAQIAVMGAKGAVEIIFRAEIGDADKVAERT
KEYEDRFLSPFVAAERGYIDEVIMPHSTRKRIARALGMLRTKEMEQPRKK
HDNIPL

Ligand information

• Ligand ID: COA
• InChI: InChI=1S/C21H36N7O16P3S/c1-21(2,16(31)19(32)24-4-3-12(29)23-5-6-48)8-41-47(38,39)44-46(36,37)40-7-11-15(43-45(33,34)35)14(30)20(42-11)28-10-27-13-17(22)25-9-26-18(13)28/h9-11,14-16,20,30-31,48H,3-8H2,1-2H3,(H,23,29)(H,24,32)(H,36,37)(H,38,39)(H2,22,25,26)(H2,33,34,35)/t11-,14-,15-,16+,20-/m1/s1
• InChIKey: RGJOEKWQDUBAIZ-IBOSZNHHSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCS)O
  CACTVS 3.341: CC(C)(CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[C@@H](O)C(=O)NCCC(=O)NCCS
  OpenEye OEToolkits 1.5.0: CC(C)(CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCS)O
  CACTVS 3.341: CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCS
  ACDLabs 10.04: O=C(NCCS)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O
• Formula: C21 H36 N7 O16 P3 S
• Name: COENZYME A
• ChEMBL: CHEMBL1213327
• DrugBank: DB01992
• ZINC: ZINC000008551087
• PDB chain: 6ybq Chain E Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ybq A new-to-nature carboxylation module to improve natural and synthetic CO2 fixation
• Resolution: 1.96 Å
• Binding residue (original residue number in PDB): I438 R441
• Binding residue (residue number reindexed from 1): I434 R437
• Annotation score: 3

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

External links

• PDB: RCSB:6ybq, PDBe:6ybq, PDBj:6ybq
• PDBsum: 6ybq
• UniProt: C5AP75