2XIJ

Crystal structure of human methylmalonyl-CoA mutase in complex with adenosylcobalamin

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Functional Information from GO Data

ChainGOidnamespacecontents
A0005759cellular_componentmitochondrial matrix
A0005739cellular_componentmitochondrion
A0031419molecular_functioncobalamin binding
A0003924molecular_functionGTPase activity
A0042802molecular_functionidentical protein binding
A0046872molecular_functionmetal ion binding
A0004494molecular_functionmethylmalonyl-CoA mutase activity
A0072341molecular_functionmodified amino acid binding
A0042803molecular_functionprotein homodimerization activity
A0009235biological_processcobalamin metabolic process
A0050667biological_processhomocysteine metabolic process
A0043547biological_processpositive regulation of GTPase activity
A0009791biological_processpost-embryonic development
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC143BINDING SITE FOR RESIDUE B12 A 800
ChainResidue
APHE138
ALEU140
AHIS143
AALA160
AVAL227
AARG228
ATHR230
AGLU268
ATRP356
AGLU392
AALA393
ALEU394
AGLY395
AGLN476
AGLY626
AHIS627
AASP628
AARG629
AGLY630
AILE634
AGLY670
ASER672
ALEU674
AALA675
AALA676
AGLY702
AGLY703
AVAL704
APHE722
AGLY723
APRO724
ATHR726
A5AD1746
AHOH2253
AHOH2447
AHOH2488
AHOH2508
AHOH3001
AHOH3002
AHOH3003
AHOH3004
AHOH3005
AHOH3006

AC210BINDING SITE FOR RESIDUE 5AD A 1746
ChainResidue
AALA160
AGLN352
ALEU396
AHOH2173
AHOH2198
AHOH2252
AHOH2507
AHOH2508
AHOH2510
AB12800

AC38BINDING SITE FOR RESIDUE SO4 A 1747
ChainResidue
AARG613
AARG613
AARG614
AARG614
AARG616
AARG616
AHOH2511
AHOH2511

AC44BINDING SITE FOR RESIDUE SO4 A 1748
ChainResidue
ATYR146
AASN150
AARG152
AHOH2512

AC54BINDING SITE FOR RESIDUE EDO A 1749
ChainResidue
ASER594
ALYS595
AGLU596
AHOH2513

AC66BINDING SITE FOR RESIDUE EDO A 1750
ChainResidue
AGLU65
AASP272
AILE274
AHOH2035
AHOH2514
AHOH2515

AC76BINDING SITE FOR RESIDUE EDO A 1751
ChainResidue
AASP58
AILE60
ATRP61
ALYS420
AHOH2030
AHOH2516

AC84BINDING SITE FOR RESIDUE EDO A 1752
ChainResidue
AARG108
ASER306
AHIS350
ASER384

AC96BINDING SITE FOR RESIDUE EDO A 1757
ChainResidue
ATHR249
AALA250
ASER258
AARG304
AHOH2190
AHOH2193

BC15BINDING SITE FOR RESIDUE EDO A 1753
ChainResidue
AGLU117
AVAL510
AGLN514
ALYS517
AHOH2517

BC27BINDING SITE FOR RESIDUE EDO A 1754
ChainResidue
ATYR110
ASER185
AMET186
ATHR216
AGLN218
ASER260
APHE308

BC33BINDING SITE FOR RESIDUE EDO A 1755
ChainResidue
APRO695
AILE697
AHOH2485

BC411BINDING SITE FOR RESIDUE BTB A 1756
ChainResidue
AILE107
AARG108
AGLN109
ATYR110
AALA111
AGLN131
ASER135
AARG406
AHOH2079
AHOH2520
AHOH2521

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
EDO_2xij_A_1750101,2-ETHANEDIOL binding site
ChainResidueligand
APRO64-GLU65EDO: 1,2-ETHANEDIOL
AASP272EDO: 1,2-ETHANEDIOL
AILE274-LEU275EDO: 1,2-ETHANEDIOL
AALA441EDO: 1,2-ETHANEDIOL
ALEU445EDO: 1,2-ETHANEDIOL
AARG467EDO: 1,2-ETHANEDIOL
ACYS471EDO: 1,2-ETHANEDIOL
AARG474EDO: 1,2-ETHANEDIOL

EDO_2xij_A_175121,2-ETHANEDIOL binding site
ChainResidueligand
ATHR101EDO: 1,2-ETHANEDIOL
ALYS420EDO: 1,2-ETHANEDIOL

BTB_2xij_A_1756142-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL binding site
ChainResidueligand
AILE107-GLY112BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
APHE122BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
AASN126BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
AGLN131BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
AGLY133-SER135BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
ASER185BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
AARG406BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

EDO_2xij_A_175291,2-ETHANEDIOL binding site
ChainResidueligand
AARG108EDO: 1,2-ETHANEDIOL
ATYR110EDO: 1,2-ETHANEDIOL
ASER306-PHE307EDO: 1,2-ETHANEDIOL
AARG348-HIS350EDO: 1,2-ETHANEDIOL
AGLN383-SER384EDO: 1,2-ETHANEDIOL

EDO_2xij_A_1754111,2-ETHANEDIOL binding site
ChainResidueligand
ATYR110EDO: 1,2-ETHANEDIOL
ASER185-THR187EDO: 1,2-ETHANEDIOL
ATHR216-GLN218EDO: 1,2-ETHANEDIOL
ASER260EDO: 1,2-ETHANEDIOL
ASER262EDO: 1,2-ETHANEDIOL
APHE308EDO: 1,2-ETHANEDIOL
AHIS350EDO: 1,2-ETHANEDIOL

EDO_2xij_A_175371,2-ETHANEDIOL binding site
ChainResidueligand
ATHR115-GLU117EDO: 1,2-ETHANEDIOL
AVAL510EDO: 1,2-ETHANEDIOL
AARG513-GLN514EDO: 1,2-ETHANEDIOL
ALYS517EDO: 1,2-ETHANEDIOL

5AD_2xij_A_174675'-DEOXYADENOSINE binding site
ChainResidueligand
AALA1375AD: 5'-DEOXYADENOSINE
AALA1605AD: 5'-DEOXYADENOSINE
ATYR264-HIS2655AD: 5'-DEOXYADENOSINE
AGLN3525AD: 5'-DEOXYADENOSINE
ALEU3965AD: 5'-DEOXYADENOSINE
AHIS6275AD: 5'-DEOXYADENOSINE

B12_2xij_A_80054COBALAMIN binding site
ChainResidueligand
APHE138B12: COBALAMIN
ALEU140B12: COBALAMIN
AHIS143B12: COBALAMIN
AALA160-GLY161B12: COBALAMIN
AVAL227-THR230B12: COBALAMIN
ATYR264-HIS265B12: COBALAMIN
AGLU268-ALA269B12: COBALAMIN
AGLY355-TRP356B12: COBALAMIN
ALEU358B12: COBALAMIN
AGLU392-LEU396B12: COBALAMIN
ALYS465B12: COBALAMIN
AGLN476B12: COBALAMIN
ALEU617B12: COBALAMIN
AVAL619B12: COBALAMIN
AGLN624-ALA631B12: COBALAMIN
AVAL633-ILE634B12: COBALAMIN
APHE638B12: COBALAMIN
AGLY670-SER672B12: COBALAMIN
ALEU674-ALA676B12: COBALAMIN
AMET700B12: COBALAMIN
AGLY702-VAL704B12: COBALAMIN
APHE722-ARG727B12: COBALAMIN
AALA731B12: COBALAMIN
AVAL735B12: COBALAMIN

EDO_2xij_A_1757121,2-ETHANEDIOL binding site
ChainResidueligand
APHE246EDO: 1,2-ETHANEDIOL
ATHR249-ALA250EDO: 1,2-ETHANEDIOL
APRO254EDO: 1,2-ETHANEDIOL
APHE256-ILE259EDO: 1,2-ETHANEDIOL
ALEU296EDO: 1,2-ETHANEDIOL
AGLU300-PHE301EDO: 1,2-ETHANEDIOL
AARG304EDO: 1,2-ETHANEDIOL

EDO_2xij_A_174941,2-ETHANEDIOL binding site
ChainResidueligand
AGLU593-GLU596EDO: 1,2-ETHANEDIOL

EDO_2xij_A_175591,2-ETHANEDIOL binding site
ChainResidueligand
AILE686EDO: 1,2-ETHANEDIOL
ALEU689EDO: 1,2-ETHANEDIOL
AARG694-VAL699EDO: 1,2-ETHANEDIOL
AGLY717EDO: 1,2-ETHANEDIOL

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
PS0054426Methylmalonyl-CoA mutase signature. R-I-A-R-N-[TQ]-x(2)-[LIVMFY](2)-x-[EQH]-E-x(4)-[KRN]-x(2)-D-P-x-[GSA]
ChainResidueDetails
AARG403-SER428

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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI11Cobalt (cobalamin axial ligand) (By similarity)
ChainResidueDetails
AHIS617

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Catalytic Information from CSA

site_idNumber of ResiduesDetails