Structure of PDB 5cjw Chain A Binding Site BS02

Receptor Information

>5cjw Chain A (length=1063) Species: 266264 (Cupriavidus metallidurans CH34)

RGPANKVRFVTAASLFDGHDASINIMRRILQSQGCEVIHLGHNRSVQEVV
TAALQEDVQGIAISSYQGGHVEYFKYMIDLLREHGGEHIQVFGGGGGVIV
PDEIRELQAYGVARIYSPEDGQRMGLAGMITDMAQRCDIDLTRYAPTTLD
TVVAGDRRALAQLITALENGKADPELVSALHAQAKAAAVPVLGITGTGGA
GKSSLTDELIRRFRLDQDDALSIAVISIDPSRRKSGGALLGDRIRMNAIN
HPNIFMRSLATREAGSEISQALPDVIAACKAARFDLVIVETSGIGQGDAA
IVPHVDLSLYVMTPEFGAASQLEKIDMLDFADFVAINKFDRKGAQDAWRD
VAKQVQRNREQWHSRAEDMPVYGTQASRFNDDGVTMLYQGLVGALGARGM
SLKPGTLPNLEGRISTGQNVIVPPARSRYLAELADTVRAYHRRVVAQSKL
ARERQQLRAAHDMLQGAGHESAALETLASERDVSLGAVERKLLAMWPQMQ
QAYSGDEYVIRTGLISTTLSGTKIRKVVLPRFEDEGEILKWLMRENVPGS
FPYTAGVFAFKREGEDPTRMFAGEGDAFRTNRRFKLVSEGMEAKRLSTAF
DSVTLYGEDPHERPDIYGKVGNSGVSIATLEDMKVLYDGFDLTNPSTSVS
MTINGPAPTILAMFMNTAIDQQIDRFRADNGRDPTADEEAKIRAWVLQNV
RGTVQADILKEDQGQNTCIFSTEFSLKVMGDIQEYFVHHQVRNFYSVSIS
GYHIAEAGANPISQLAFTLANGFTYVEAYLARGMHIDDFAPNLSFFFSNG
MDPEYSVLGRVARRIWAVTMRDKYGANDRSQKLKYHIQTSGRSLHAQEID
FNDIRTTLQALIAIYDNCNSLHTNAYDEAITTPTAESVRRALAIQLIINR
EWGVAKCENPNQGSFLIEELTDLVEEAVLQEFERIAERGGVLGAMETGYQ
RGKIQEESLYYEQLKHDGTLPIIGVNTFRNPNGDQTLELARSSEDEKQSQ
LHRLTEFHGAHQADAEAMLARLRQAVIDNRNVFAVLMDAVRVCSLGQITH
ALFEVGGQYRRNM

Ligand information

• Ligand ID: 52O
• InChI: InChI=1S/C26H44N7O17P3S/c1-25(2,3)24(38)54-9-8-28-15(34)6-7-29-22(37)19(36)26(4,5)11-47-53(44,45)50-52(42,43)46-10-14-18(49-51(39,40)41)17(35)23(48-14)33-13-32-16-20(27)30-12-31-21(16)33/h12-14,17-19,23,35-36H,6-11H2,1-5H3,(H,28,34)(H,29,37)(H,42,43)(H,44,45)(H2,27,30,31)(H2,39,40,41)/t14-,17-,18-,19+,23-/m1/s1
• InChIKey: FCMKBHDFOPWWQK-NDZSKPAWSA-N
• SMILES:
  CACTVS 3.385: CC(C)(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
  OpenEye OEToolkits 1.9.2: CC(C)(C)C(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
  OpenEye OEToolkits 1.9.2: CC(C)(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
  CACTVS 3.385: CC(C)(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 12.01: OC3C(n1c2c(nc1)c(N)ncn2)OC(COP(OP(OCC(C)(C(O)C(NCCC(NCCSC(C(C)(C)C)=O)=O)=O)C)(=O)O)(O)=O)C3OP(O)(=O)O
• Formula: C26 H44 N7 O17 P3 S
• Name: pivalyl-coenzyme A
• ZINC: ZINC000195883426
• PDB chain: 5cjw Chain A Residue 1103

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5cjw 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): F558 F560 R562 R569 F571 R595 S650 T652 R701 T703 Q705 Y745 Y752 H753 S794 F796 R829 K834 H836
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): K26 F598 Y779 H780
• Catalytic site (residue number reindexed from 1): K6 F571 Y752 H753
• 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:5cjw, PDBe:5cjw, PDBj:5cjw
• PDBsum: 5cjw
• PubMed: 26318610
• UniProt: Q1LRY0|ICMF_CUPMC Fused isobutyryl-CoA mutase (Gene Name=icmF)