Structure of PDB 4r3u Chain B Binding Site BS03

Receptor Information
>4r3u Chain B (length=555) Species: 391953 (Aquincola tertiaricarbonis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TWLEPQIKSQLQSERKDWEANEVGAFLKKAPERKEQFHTIGDFPVQRTYT
AADIADTPLEDIGLPGRYPFTRGPYPTMYRSRTWTMRQIAGFGTGEDTNK
RFKYLIAQGQTGISTDFDMPTLMGYDSDHPMSDGEVGREGVAIDTLADME
ALLADIDLEKISVSFTINPSAWILLAMYVALGEKRGYDLNKLSGTVQADI
LKEYMAQKEYIYPIAPSVRIVRDIITYSAKNLKRYNPINISGYHISEAGS
SPLQEAAFTLANLITYVNEVTKTGMHVDEFAPRLAFFFVSQGDFFEEVAK
FRALRRCYAKIMKERFGARNPESMRLRFHCQTAAATLTKPQYMVNVVRTS
LQALSAVLGGAQSLHTNGYDEAFAIPTEDAMKMALRTQQIIAEESGVADV
IDPLGGSYYVEALTTEYEKKIFEILEEVEKRGGTIKLIEQGWFQKQIADF
AYETALRKQSGQKPVIGVNRFVENEVKIEIHPYDNTTAERQISRTRRVRA
ERDEAKVQAMLDQLVAVAKDESQNLMPLTIELVKAGATMGDIVEKLKGIW
GTYRE
Ligand information
Ligand IDB12
InChIInChI=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
InChIKeyLKVIQTCSMMVGFU-DWSMJLPVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1cc2c(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
FormulaC62 H89 Co N13 O14 P
NameCOBALAMIN
ChEMBL
DrugBank
ZINC
PDB chain4r3u Chain D Residue 800 [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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PDB4r3u Structural basis of the stereospecificity of bacterial B12-dependent 2-hydroxyisobutyryl-CoA mutase.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		D117 M120 E140 Q208 E210 H245 E248 A335 E372 A373 A375
Binding residue
(residue number reindexed from 1)		D116 M119 E139 Q207 E209 H244 E247 A334 E371 A372 A374
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) I90 Y244 H245
Catalytic site (residue number reindexed from 1) I89 Y243 H244
Enzyme Commision number 5.4.99.64: 2-hydroxyisobutanoyl-CoA mutase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004494 methylmalonyl-CoA mutase activity
GO:0016853 isomerase activity
GO:0016866 intramolecular transferase activity
GO:0031419 cobalamin binding

View graph for
Molecular Function
External links
PDB RCSB:4r3u, PDBe:4r3u, PDBj:4r3u
PDBsum4r3u
PubMed25720495
UniProtI3VE77|HCMA_AQUTE 2-hydroxyisobutanoyl-CoA mutase large subunit (Gene Name=hcmA)

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