SMTL ID : 8gju.2 (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 COA: COENZYME A(Non-covalent)

COA.1: 24 residues within 4Å: Chain A: Y.86, T.88, M.89, F.92, R.93, T.96, R.98, S.125, S.173, 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, S.374 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:Y.86, A:Y.86, A:T.88, A:T.88, A:T.96, A:T.96, A:R.98, A:S.173, A:S.175, A:N.247, A:S.250, A:S.250, A:S.296, A:S.296, A:R.338, A:H.340, A:S.374 Salt bridges: A:R.93, A:R.93, A:R.98, A:R.294 COA.6: 23 residues within 4Å: Chain D: Y.86, T.88, M.89, F.92, 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, S.374 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:T.206, D:R.338 Hydrogen bonds: D:Y.86, D:T.88, D:M.89, D:R.93, D:T.96, D:S.125, D:S.175, D:T.206, D:S.250, D:S.250, D:S.296, D:R.338, D:S.374 Salt bridges: D:R.98, D:R.294

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

GDP.2: 15 residues within 4Å: Chain B: 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 Ligands: MG.3 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:P.82, B:G.84, B:A.85, 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 Water bridges: B:S.88, B:S.88 Salt bridges: B:K.87, B:D.223 GDP.4: 16 residues within 4Å: Chain B: D.201, Q.204 Chain C: 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.5 21 PLIP interactions: 2 interactions with chain B, 19 interactions with chain C Hydrogen bonds: B:D.201, C:G.84, C:G.86, C:K.87, C:S.88, C:T.89, C:T.89, C:E.173, C:K.221, C:K.221, C:A.260, C:R.261, C:R.261 Salt bridges: B:D.201, C:K.87, C:R.127, C:D.223 Water bridges: C:S.88, C:E.173 pi-Cation interactions: C:R.261, C:R.261

2 x MG: MAGNESIUM ION(Non-covalent)

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

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

Methylmalonyl-CoA mutase, mitochondrial: AD
Methylmalonic aciduria type A protein, mitochondrial: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

D
H

B
A

C
B

Methylmalonyl-CoA mutase, mitochondrial

Methylmalonic aciduria type A protein, mitochondrial

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