Structure of PDB 5cjt Chain A Binding Site BS01

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: B12
• InChI: InChI=1S/C62H90N13O14P.Co/c1-29-20-39-40(21-30(29)2)75(28-70-39)57-52(84)53(41(27-76)87-57)89-90(85,86)88-31(3)26-69-49(83)18-19-59(8)37(22-46(66)80)56-62(11)61(10,25-48(68)82)36(14-17-45(65)79)51(74-62)33(5)55-60(9,24-47(67)81)34(12-15-43(63)77)38(71-55)23-42-58(6,7)35(13-16-44(64)78)50(72-42)32(4)54(59)73-56;/h20-21,23,28,31,34-37,41,52-53,56-57,72,76,84H,12-19,22,24-27H2,1-11H3,(H2,63,77)(H2,64,78)(H2,65,79)(H2,66,80)(H2,67,81)(H2,68,82)(H,69,83)(H,85,86);/q;+2/b42-23-,50-32-,55-33-;/t31-,34-,35-,36-,37+,41-,52-,53-,56-,57+,59-,60+,61+,62+;/m1./s1
• InChIKey: LKVIQTCSMMVGFU-DWSMJLPVSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: Cc1cc2c(cc1C)n(cn2)C3C(C(C(O3)CO)OP(=O)(O)OC(C)CNC(=O)CCC4(C(C5C6(C(C(C7=[N]6[Co+2]89[N]5=C4C(=C1[NH]8C(=CC2=[N]9C(=C7C)C(C2CCC(=O)N)(C)CC(=O)N)C(C1CCC(=O)N)(C)C)C)CCC(=O)N)(C)CC(=O)N)C)CC(=O)N)C)O
  CACTVS 3.370: [Co++]|1|2|3|N4C5=CC6=N|1C(=C(C)C7=N|2[C](C)([CH]8N|3=C(C(=C4[CH](CCC(N)=O)C5(C)C)C)[C](C)(CCC(=O)NC[CH](C)O[P](O)(=O)O[CH]9[CH](O)[CH](O[CH]9CO)n%10cnc%11cc(C)c(C)cc%10%11)[CH]8CC(N)=O)[C](C)(CC(N)=O)[CH]7CCC(N)=O)[C](C)(CC(N)=O)[CH]6CCC(N)=O
  CACTVS 3.370: [Co++]|1|2|3|N4C5=CC6=N|1C(=C(C)C7=N|2[C@@](C)([C@@H]8N|3=C(C(=C4[C@@H](CCC(N)=O)C5(C)C)C)[C@](C)(CCC(=O)NC[C@@H](C)O[P](O)(=O)O[C@H]9[C@@H](O)[C@H](O[C@@H]9CO)n%10cnc%11cc(C)c(C)cc%10%11)[C@H]8CC(N)=O)[C@@](C)(CC(N)=O)[C@@H]7CCC(N)=O)[C@@](C)(CC(N)=O)[C@@H]6CCC(N)=O
• Formula: C62 H89 Co N13 O14 P
• Name: COBALAMIN
• PDB chain: 5cjt Chain A Residue 1101

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): G38 H39 D40 A41 S42 M46 Y86 Q87 G114 G116 V118 Y136 S137 F627 L632 S650 Q742 H780 E783 A784 G868 R869 E905 A906 T908 H993
• Binding residue (residue number reindexed from 1): G18 H19 D20 A21 S22 M26 Y66 Q67 G94 G96 V98 Y116 S117 F598 L603 S621 Q713 H751 E754 A755 G839 R840 E876 A877 T879 H964
• Annotation score: 1

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)