Structure of PDB 5cjv Chain B Binding Site BS02

Receptor Information
>5cjv Chain B (length=1059) Species: 266264 (Cupriavidus metallidurans CH34) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GPANKVRFVTAASLFDGHDASINIMRRILQSQGCEVIHLGHNRSVQEVVT
AALQEDVQGIAISSYQGGHVEYFKYMIDLLREHGGEHIQVFGGGGGVIVP
DEIRELQAYGVARIYSPEDGQRMGLAGMITDMAQRCDIDLTRYAPTTLDT
VVAGDRRALAQLITALENGKADPELVSALHAQAKAAAVPVLGITGTGGAG
KSSLTDELIRRFRLDQDDALSIAVISIDPSRRKSGGALLGDRIRMNAINH
PNIFMRSLATREAGSEISQALPDVIAACKAARFDLVIVETSGIGQGDAAI
VPHVDLSLYVMTPEFGAASQLEKIDMLDFADFVAINKFDRKGAQDAWRDV
AKQVQRNREQWHSRAEDMPVYGTQASRFNDDGVTMLYQGLVGALGARGMS
LKPGTLPNLEGRISTGQNVIVPPARSRYLAELADTVRAYHRRVVAQSKLA
RERQQLRAAHDMLQGAGHESAALETLASERDVSLGAVERKLLAMWPQMQQ
AYSGDEYVVKIRDKEIRTGLISTTLSGTKIRKVVLPRFEDEGEILKWLMR
ENVPGSFPYTAGVFAFKREGPTRMFAGEGDAFRTNRRFKLVSEGMEAKRL
STAFDSVTLYGEDPHERPDIYGKVGNSGVSIATLEDMKVLYDGFDLTNPS
TSVSMTINGPAPTILAMFMNTAIDQQIDRFRADNGRDPTADEEAKIRAWV
LQNVRGTVQADILKEDQGQNTCIFSTEFSLKVMGDIQEYFVHHQVRNFYS
VSISGYHIAEAGANPISQLAFTLANGFTYVEAYLARGMHIDDFAPNLSFF
FSNGMDPEYSVLGRVARRIWAVTMRDKYGANDRSQKLKYHIQTSGRSLHA
QEIDFNDIRTTLQALIAIYDNCNSLHTNAYITTPTAESVRRALAIQLIIN
REWGVAKCENPNQGSFLIEELTDLVEEAVLQEFERIAERGGVLGAMETGY
QRGKIQEESLYYEQLKHDGTLPIIGVNTFRNPNGLARSSEDEKQSQLHRL
TEFHGAHQADAEAMLARLRQAVIDNRNVFAVLMDAVRVCSLGQITHALFE
VGGQYRRNM
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain5cjv Chain B Residue 1103 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5cjv Structural Basis for Substrate Specificity in Adenosylcobalamin-dependent Isobutyryl-CoA Mutase and Related Acyl-CoA Mutases.
Resolution3.45 Å
Binding residue
(original residue number in PDB)		G219 G221 K222 S223 S224 R265 K358 D360 Q395 S397 E973 N1092
Binding residue
(residue number reindexed from 1)		G198 G200 K201 S202 S203 R244 K337 D339 Q374 S376 E947 N1058
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) K26 F598 Y779 H780
Catalytic site (residue number reindexed from 1) K5 F575 Y756 H757
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5cjv, PDBe:5cjv, PDBj:5cjv
PDBsum5cjv
PubMed26318610
UniProtQ1LRY0|ICMF_CUPMC Fused isobutyryl-CoA mutase (Gene Name=icmF)

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