Structure of PDB 5cjt Chain A Binding Site BS02

Receptor Information

>5cjt Chain A (length=1062) Species: 266264 (Cupriavidus metallidurans CH34)

RGPANKVRFVTAASLFDGHDASINIMRRILQSQGCEVIHLGHNRSVQEVV
TAALQEDVQGIAISSYQGGHVEYFKYMIDLLREHGGEHIQVFGGGGGVIV
PDEIRELQAYGVARIYSPEDGQRMGLAGMITDMAQRCDIDLTRYAPTTLD
TVVAGDRRALAQLITALENGKADPELVSALHAQAKAAAVPVLGITGTGGA
GKSSLTDELIRRFRLDQDDALSIAVISIDPSRRKSGGALLGDRIRMNAIN
HPNIFMRSLATREASEISQALPDVIAACKAARFDLVIVETSGIGQGDAAI
VPHVDLSLYVMTPEFGAASQLEKIDMLDFADFVAINKFDRKGAQDAWRDV
AKQVQRNREQWHSRAEDMPVYGTQASRFNDDGVTMLYQGLVGALGARGMS
LKPGTLPNLEGRISTGQNVIVPPARSRYLAELADTVRAYHRRVVAQSKLA
RERQQLRAAHDMLQGAGHESAALETLASERDVSLGAVERKLLAMWPQMQQ
AYSGDEYVRTGLISTTLSGTKIRKVVLPRFEDEGEILKWLMRENVPGSFP
YTAGVFAFKREGEDPTRMFAGEGDAFRTNRRFKLVSEGMEAKRLSTAFDS
VTLYGEDPHERPDIYGKVGNSGVSIATLEDMKVLYDGFDLTNPSTSVSMT
INGPAPTILAMFMNTAIDQQIDRFRADNGRDPTADEEAKIRAWVLQNVRG
TVQADILKEDQGQNTCIFSTEFSLKVMGDIQEYFVHHQVRNFYSVSISGY
HIAEAGANPISQLAFTLANGFTYVEAYLARGMHIDDFAPNLSFFFSNGMD
PEYSVLGRVARRIWAVTMRDKYGANDRSQKLKYHIQTSGRSLHAQEIDFN
DIRTTLQALIAIYDNCNSLHTNAYDEAITTPTAESVRRALAIQLIINREW
GVAKCENPNQGSFLIEELTDLVEEAVLQEFERIAERGGVLGAMETGYQRG
KIQEESLYYEQLKHDGTLPIIGVNTFRNPNGDPQTLELARSSEDEKQSQL
HRLTEFHGAHQADAEAMLARLRQAVIDNRNVFAVLMDAVRVCSLGQITHA
LFEVGGQYRRNM

Ligand information

• Ligand ID: CO6
• InChI: InChI=1S/C25H42N7O17P3S/c1-13(2)24(37)53-8-7-27-15(33)5-6-28-22(36)19(35)25(3,4)10-46-52(43,44)49-51(41,42)45-9-14-18(48-50(38,39)40)17(34)23(47-14)32-12-31-16-20(26)29-11-30-21(16)32/h11-14,17-19,23,34-35H,5-10H2,1-4H3,(H,27,33)(H,28,36)(H,41,42)(H,43,44)(H2,26,29,30)(H2,38,39,40)/t14-,17-,18-,19+,23-/m1/s1
• InChIKey: AEWHYWSPVRZHCT-NDZSKPAWSA-N
• SMILES:
  CACTVS 3.341: CC(C)C(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(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
  CACTVS 3.341: CC(C)C(=O)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
  ACDLabs 10.04: O=C(SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O)C(C)C
  OpenEye OEToolkits 1.5.0: CC(C)C(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
  OpenEye OEToolkits 1.5.0: CC(C)C(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(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)O
• Formula: C25 H42 N7 O17 P3 S
• Name: ISOBUTYRYL-COENZYME A;
  IB-CO6
• PDB chain: 5cjt Chain A Residue 1103

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5cjt Structural Basis for Substrate Specificity in Adenosylcobalamin-dependent Isobutyryl-CoA Mutase and Related Acyl-CoA Mutases.
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): F585 F587 R589 R596 F598 R622 S677 T679 R728 T730 Q732 Y772 Y779 H780 S821 F823 R856 K861 H863
• Binding residue (residue number reindexed from 1): F556 F558 R560 R567 F569 R593 S648 T650 R699 T701 Q703 Y743 Y750 H751 S792 F794 R827 K832 H834
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): K26 F598 Y779 H780
• Catalytic site (residue number reindexed from 1): K6 F569 Y750 H751
• Enzyme Commision number: 3.6.5.-
  5.4.99.13: isobutyryl-CoA mutase.

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003824 catalytic activity
• GO:0003924 GTPase activity
• GO:0004494 methylmalonyl-CoA mutase activity
• GO:0005525 GTP binding
• GO:0016787 hydrolase activity
• GO:0016853 isomerase activity
• GO:0016866 intramolecular transferase activity
• GO:0031419 cobalamin binding
• GO:0034784 pivalyl-CoA mutase activity
• GO:0046872 metal ion binding
• GO:0047727 isobutyryl-CoA mutase activity

Biological Process

• GO:0006637 acyl-CoA metabolic process

External links

• PDB: RCSB:5cjt, PDBe:5cjt, PDBj:5cjt
• PDBsum: 5cjt
• PubMed: 26318610
• UniProt: Q1LRY0|ICMF_CUPMC Fused isobutyryl-CoA mutase (Gene Name=icmF)