Structure of PDB 4xc6 Chain A Binding Site BS02

Receptor Information
>4xc6 Chain A (length=1067) Species: 266264 (Cupriavidus metallidurans CH34) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RGPANKVRFVTAASLFDGHDASINIMRRILQSQGCEVIHLGHNRSVQEVV
TAALQEDVQGIAISSYQGGHVEYFKYMIDLLREHGGEHIQVFGGGGGVIV
PDEIRELQAYGVARIYSPEDGQRMGLAGMITDMAQRCDIDLTRYAPTTLD
TVVAGDRRALAQLITALENGKADPELVSALHAQAKAAAVPVLGITGTGGA
GKSSLTDELIRRFRLDQDDALSIAVISIDPSRRKSGGALLGDRIRMNAIN
HPNIFMRSLATREAGSEISQALPDVIAACKAARFDLVIVETSGIGQGDAA
IVPHVDLSLYVMTPEFGAASQLEKIDMLDFADFVAINKFDRKGAQDAWRD
VAKQVQRNREQWHSRAEDMPVYGTQASRFNDDGVTMLYQGLVGALGARGM
SLKPGTLPNLEGRISTGQNVIVPPARSRYLAELADTVRAYHRRVVAQSKL
ARERQQLRAAHDMLQGAGHESAALETLASERDVSLGAVERKLLAMWPQMQ
QAYSGDEYVVIRTGLISTTLSGTKIRKVVLPRFEDEGEILKWLMRENVPG
SFPYTAGVFAFKREGEDPTRMFAGEGDAFRTNRRFKLVSEGMEAKRLSTA
FDSVTLYGEDPHERPDIYGKVGNSGVSIATLEDMKVLYDGFDLTNPSTSV
SMTINGPAPTILAMFMNTAIDQQIDRFRADNGRDPTADEEAKIRAWVLQN
VRGTVQADILKEDQGQNTCIFSTEFSLKVMGDIQEYFVHHQVRNFYSVSI
SGYHIAEAGANPISQLAFTLANGFTYVEAYLARGMHIDDFAPNLSFFFSN
GMDPEYSVLGRVARRIWAVTMRDKYGANDRSQKLKYHIQTSGRSLHAQEI
DFNDIRTTLQALIAIYDNCNSLHTNAYDEAITTPTAESVRRALAIQLIIN
REWGVAKCENPNQGSFLIEELTDLVEEAVLQEFERIAERGGVLGAMETGY
QRGKIQEESLYYEQLKHDGTLPIIGVNTFRNPNGDPTPQTLELARSSEDE
KQSQLHRLTEFHGAHQADAEAMLARLRQAVIDNRNVFAVLMDAVRVCSLG
QITHALFEVGGQYRRNM
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 chain4xc6 Chain A 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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PDB4xc6 Visualization of a radical B12 enzyme with its G-protein chaperone.
Resolution3.35 Å
Binding residue
(original residue number in PDB)		G219 G221 K222 S223 S224 R265 N357 K358 D360 Q395 S397 E973
Binding residue
(residue number reindexed from 1)		G199 G201 K202 S203 S204 R245 N337 K338 D340 Q375 S377 E947
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) K26 F598 Y779 H780
Catalytic site (residue number reindexed from 1) K6 F572 Y753 H754
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:4xc6, PDBe:4xc6, PDBj:4xc6
PDBsum4xc6
PubMed25675500
UniProtQ1LRY0|ICMF_CUPMC Fused isobutyryl-CoA mutase (Gene Name=icmF)

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