SMTL ID : 8gju.1 (1 other biounit)

Crystal structure of human methylmalonyl-CoA mutase (MMUT) in complex with methylmalonic acidemia type A protein (MMAA), coenzyme A, and GDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.79 Å

Oligo State

hetero-2-2-mer

Ligands

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 17 residues within 4Å: Chain A: P.82, G.84, A.85, G.86, K.87, S.88, T.89, R.127, E.173, K.221, D.223, S.259, A.260, R.261 Chain B: D.201, E.202 Ligands: MG.2 21 PLIP interactions: 19 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:P.82, A:G.84, A:A.85, A:G.86, A:K.87, A:S.88, A:S.88, A:T.89, A:T.89, A:K.221, A:K.221, A:A.260, A:R.261, A:R.261, B:D.201 Water bridges: A:E.173, A:E.173 Salt bridges: A:K.87, A:R.127, A:D.223, B:D.201 GDP.3: 15 residues within 4Å: Chain A: D.201 Chain B: G.84, A.85, G.86, K.87, S.88, T.89, R.127, E.173, K.221, D.223, S.259, A.260, R.261 Ligands: MG.4 22 PLIP interactions: 21 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:P.82, B:G.84, B:A.85, B:G.86, B:G.86, B:K.87, B:S.88, B:T.89, B:T.89, B:K.221, B:K.221, B:A.260, B:R.261, B:R.261, A:D.201 Water bridges: B:S.88, B:R.127 Salt bridges: B:K.87, B:R.127, B:D.223 pi-Cation interactions: B:R.261, B:R.261

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: S.88, D.124, E.173 Ligands: GDP.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.88, A:D.124, A:E.173, H2O.1, H2O.1 MG.4: 4 residues within 4Å: Chain B: S.88, D.124, E.173 Ligands: GDP.3 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.88, B:D.124, B:E.173, H2O.1

2 x COA: COENZYME A(Non-covalent)

COA.5: 22 residues within 4Å: Chain C: Y.86, P.87, T.88, M.89, R.93, T.96, R.98, S.125, S.175, M.176, T.177, T.206, Q.208, N.247, S.250, R.294, S.296, F.298, R.338, A.339, H.340, Q.373 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:R.338 Hydrogen bonds: C:Y.86, C:T.88, C:T.88, C:T.88, C:M.89, C:T.96, C:S.175, C:T.206, C:N.247, C:S.250, C:S.250, C:S.296, C:R.338 Salt bridges: C:R.98, C:R.294 COA.6: 20 residues within 4Å: Chain D: Y.86, T.88, M.89, R.93, T.96, R.98, S.173, S.175, M.176, T.177, T.206, Q.208, N.247, S.250, R.294, S.296, R.338, A.339, H.340, Q.373 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:R.338 Hydrogen bonds: D:Y.86, D:Y.86, D:T.88, D:T.88, D:M.89, D:T.96, D:T.96, D:S.173, D:S.175, D:T.206, D:N.247, D:S.250, D:S.250, D:S.296 Salt bridges: D:R.98, D:R.294

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mascarenhas, R. et al., Architecture of the human G-protein-methylmalonyl-CoA mutase nanoassembly for B 12 delivery and repair. Nat Commun (2023)

Release Date

2023-08-09

Peptides

Methylmalonic aciduria type A protein, mitochondrial: AB
Methylmalonyl-CoA mutase, mitochondrial: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
F

C
J

D
K

Methylmalonic aciduria type A protein, mitochondrial

Methylmalonyl-CoA mutase, mitochondrial

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