Structure of PDB 8dyj Chain B Binding Site BS02

Receptor Information
>8dyj Chain B (length=708) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QPLHPEWAALAKKQLKGKNPEDLIWHTPEGISIKPLYSKRDTMDLPEELP
GVKPFTRGPYPTMYTFRPWTIRQYAGFSTVEESNKFYKDNIKAGQQGLSV
AFDLATHRGYDSDNPRVRGDVGMAGVAIDTVEDTKILFDGIPLEKMSVSM
TMNGAVIPVLANFIVTGEEQGVPKEKLTGTIQNDILKEFMVRNTYIFPPE
PSMKIIADIFEYTAKHMPKFNSISISGYHMQEAGADAILELAYTLADGLE
YSRTGLQAGLTIDEFAPRLSFFWGIGMNFYMEIAKMRAGRRLWAHLIEKM
FQPKNSKSLLLRAHCQTSGWSLTEQDPYNNIVRTAIEAMAAVFGGTQSLH
TNSFDEALGLPTVKSARIARNTQIIIQEESGIPKVADPWGGSYMMECLTN
DVYDAALKLINEIEEMGGMAKAVAEGIPKLRIEECAARRQARIDSGSEVI
VGVNKYQLEKEDTVEVLAIDNTSVRNRQIEKLKKIKSSRDQALAERCLAA
LTECAASGDGNILALAVDASRARCTVGEITDALKKVFGEHKANDRMVSGA
YRQEFGESKEITSAIKRVHKFMEREGRRPRLLVAKMGQDGHDRGAKVIAT
GFADLGFDVDIGPLFQTPREVAQQAVDADVHAVGVSTLAAGHKTLVPELI
KELNSLGRPDILVMCGGVIPPQDYEFLFEVGVSNVFGPGTRIPKAAVQVL
DDIEKCLE
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain8dyj Chain B Residue 802 [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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PDB8dyj Bivalent molecular mimicry by ADP protects metal redox state and promotes coenzyme B 12 repair.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		Y73 T150 R191 Y227 H228 F271 Q315 N351 E355 L359 P360
Binding residue
(residue number reindexed from 1)		Y74 T151 R192 Y228 H229 F272 Q316 N352 E356 L360 P361
Annotation score2
Enzymatic activity
Enzyme Commision number 5.4.99.2: methylmalonyl-CoA mutase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0003924 GTPase activity
GO:0004494 methylmalonyl-CoA mutase activity
GO:0005515 protein binding
GO:0016853 isomerase activity
GO:0016866 intramolecular transferase activity
GO:0031419 cobalamin binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
GO:0072341 modified amino acid binding
Biological Process
GO:0006790 sulfur compound metabolic process
GO:0009791 post-embryonic development
GO:0019678 propionate metabolic process, methylmalonyl pathway
GO:0043547 positive regulation of GTPase activity
GO:0050667 homocysteine metabolic process
GO:1901290 succinyl-CoA biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8dyj, PDBe:8dyj, PDBj:8dyj
PDBsum8dyj
PubMed36888659
UniProtP22033|MUTA_HUMAN Methylmalonyl-CoA mutase, mitochondrial (Gene Name=MMUT)

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