Structure of PDB 8dyj Chain B

Receptor sequence

>8dyjB (length=708) Species: 9606 (Homo sapiens)

QPLHPEWAALAKKQLKGKNPEDLIWHTPEGISIKPLYSKRDTMDLPEELP
GVKPFTRGPYPTMYTFRPWTIRQYAGFSTVEESNKFYKDNIKAGQQGLSV
AFDLATHRGYDSDNPRVRGDVGMAGVAIDTVEDTKILFDGIPLEKMSVSM
TMNGAVIPVLANFIVTGEEQGVPKEKLTGTIQNDILKEFMVRNTYIFPPE
PSMKIIADIFEYTAKHMPKFNSISISGYHMQEAGADAILELAYTLADGLE
YSRTGLQAGLTIDEFAPRLSFFWGIGMNFYMEIAKMRAGRRLWAHLIEKM
FQPKNSKSLLLRAHCQTSGWSLTEQDPYNNIVRTAIEAMAAVFGGTQSLH
TNSFDEALGLPTVKSARIARNTQIIIQEESGIPKVADPWGGSYMMECLTN
DVYDAALKLINEIEEMGGMAKAVAEGIPKLRIEECAARRQARIDSGSEVI
VGVNKYQLEKEDTVEVLAIDNTSVRNRQIEKLKKIKSSRDQALAERCLAA
LTECAASGDGNILALAVDASRARCTVGEITDALKKVFGEHKANDRMVSGA
YRQEFGESKEITSAIKRVHKFMEREGRRPRLLVAKMGQDGHDRGAKVIAT
GFADLGFDVDIGPLFQTPREVAQQAVDADVHAVGVSTLAAGHKTLVPELI
KELNSLGRPDILVMCGGVIPPQDYEFLFEVGVSNVFGPGTRIPKAAVQVL
DDIEKCLE

3D structure

• PDB: 8dyj Bivalent molecular mimicry by ADP protects metal redox state and promotes coenzyme B 12 repair.
• Chain: B
• Resolution: 2.2 Å

Enzymatic activity

• Enzyme Commision number: 5.4.99.2: methylmalonyl-CoA mutase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	B12	B	F101 L103 H106 A123 V190 R191 H228 E231 G318 W319 E355 G358 L359 G589 H590 D591 R592 G593 I597 S635 L637 A639 G665 G666 V667 F685 G686 T689	F102 L104 H107 A124 V191 R192 H229 E232 G319 W320 E356 G359 L360 G590 H591 D592 R593 G594 I598 S636 L638 A640 G666 G667 V668 F686 G687 T690
BS02	ADP	B	Y73 T150 R191 Y227 H228 F271 Q315 N351 E355 L359 P360	Y74 T151 R192 Y228 H229 F272 Q316 N352 E356 L360 P361

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

External links

• PDB: RCSB:8dyj, PDBe:8dyj, PDBj:8dyj
• PDBsum: 8dyj
• PubMed: 36888659
• UniProt: P22033|MUTA_HUMAN Methylmalonyl-CoA mutase, mitochondrial (Gene Name=MMUT)