Structure of PDB 2xiq Chain B Binding Site BS02

Receptor Information

>2xiq Chain B (length=713) Species: 9606 (Homo sapiens)

QQPLHPEWAALAKKQLKGKNPEDLIWHTPEGISIKPLYSKRDTMDLPEEL
PGVKPFTRGPYPTMYTFRPWTIRQYAGFSTVEESNKFYKDNIKAGQQGLS
VAFDLATHRGYDSDNPRVRGDVGMAGVAIDTVEDTKILFDGIPLEKMSVS
MTMNGAVIPVLANFIVTGEEQGVPKEKLTGTIQNDILKEFMVRNTYIFPP
EPSMKIIADIFEYTAKHMPKFNSISISGYHMQEAGADAILELAYTLADGL
EYSRTGLQAGLTIDEFAPRLSFFWGIGMNFYMEIAKMRAGRRLWAHLIEK
MFQPKNSKSLLLRAHCQTSGWSLTEQDPYNNIVRTAIEAMAAVFGGTQSL
HTNSFDEALGLPTVKSARIARNTQIIIQEESGIPKVADPWGGSYMMECLT
NDVYDAALKLINEIEEMGGMAKAVAEGIPKLRIEECAARRQARIDSGSEV
IVGVNKYQLEKEDTVEVLAIDNTSVRNRQIEKLKKIKSSRDQALAERCLA
ALTECAASGDGNILALAVDASRARCTVGEITDALKKVFGEHKANDRMVSG
AYRQEFGESKEITSAIKRVHKFMEREGRRPRLLVAKMGQDGHDRGAKVIA
TGFADLGFDVDIGPLFQTPREVAQQAVDADVHAVGVSTLAAGHKTLVPEL
IKELNSLGRPDILVMCGGVIPPQDYEFLFEVGVSNVFGPGTRIPKAAVQV
LDDIEKCLEKKQQ

Ligand information

• Ligand ID: MLC
• InChI: InChI=1S/C24H38N7O19P3S/c1-24(2,19(37)22(38)27-4-3-13(32)26-5-6-54-15(35)7-14(33)34)9-47-53(44,45)50-52(42,43)46-8-12-18(49-51(39,40)41)17(36)23(48-12)31-11-30-16-20(25)28-10-29-21(16)31/h10-12,17-19,23,36-37H,3-9H2,1-2H3,(H,26,32)(H,27,38)(H,33,34)(H,42,43)(H,44,45)(H2,25,28,29)(H2,39,40,41)/t12-,17-,18-,19+,23-/m1/s1
• InChIKey: LTYOQGRJFJAKNA-DVVLENMVSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCSC(=O)CC(=O)O)O
  OpenEye OEToolkits 1.5.0: CC(C)(CO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCSC(=O)CC(=O)O)O
  CACTVS 3.341: CC(C)(CO[P@](O)(=O)O[P@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[C@@H](O)C(=O)NCCC(=O)NCCSC(=O)CC(O)=O
  ACDLabs 10.04: O=C(O)CC(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O
  CACTVS 3.341: CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCSC(=O)CC(O)=O
• Formula: C24 H38 N7 O19 P3 S
• Name: MALONYL-COENZYME A
• ChEMBL: CHEMBL1234355
• DrugBank: DB04524
• ZINC: ZINC000008551112
• PDB chain: 2xiq Chain B Residue 5001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2xiq Structures of the Human Gtpase Mmaa and Vitamin B12-Dependent Methylmalonyl-Coa Mutase and Insight Into Their Complex Formation.
• Resolution: 1.95 Å
• Binding residue (original residue number in PDB): Y96 T98 M99 R103 T106 R108 Y110 S185 T187 T216 Q218 R228 K255 H265 R304 S306 F308 A349 H350 Q352 Q383
• Binding residue (residue number reindexed from 1): Y61 T63 M64 R68 T71 R73 Y75 S150 T152 T181 Q183 R193 K220 H230 R269 S271 F273 A314 H315 Q317 Q348
• Annotation score: 3

Enzymatic activity

• Catalytic site (original residue number in PDB): Y110 Y264 H265 K621 D625 H627
• Catalytic site (residue number reindexed from 1): Y75 Y229 H230 K586 D590 H592
• 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

External links

• PDB: RCSB:2xiq, PDBe:2xiq, PDBj:2xiq
• PDBsum: 2xiq
• PubMed: 20876572
• UniProt: P22033|MUTA_HUMAN Methylmalonyl-CoA mutase, mitochondrial (Gene Name=MMUT)