SMTL ID : 8dyl.1

Crystal structure of human methylmalonyl-CoA mutase bound to aquocobalamin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x B12: COBALAMIN(Non-covalent)

B12.1: 36 residues within 4Å: Chain A: L.130, A.150, V.217, R.218, T.220, E.258, A.259, G.345, W.346, E.382, A.383, L.384, G.385, Q.466, D.615, G.616, H.617, D.618, R.619, G.620, I.624, F.628, G.660, S.662, L.664, A.665, A.666, G.692, G.693, V.694, F.712, G.713, P.714, G.715, T.716 Ligands: GOL.6 26 PLIP interactions: 25 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:A.150, A:R.218, A:A.259, A:I.624, A:I.624, A:F.628, A:F.712, A:F.712 Hydrogen bonds: A:A.150, A:R.218, A:R.218, A:G.385, A:G.616, A:H.617, A:D.618, A:D.618, A:R.619, A:G.620, A:A.665, A:G.693, A:G.715, A:T.716 Water bridges: A:A.383, A:Q.466 Metal complexes: A:H.617, H2O.6

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain A: I.97, R.98, Q.99, Y.100, A.101, F.112, N.116, S.125, R.396 Ligands: GOL.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:I.97, A:Q.99, A:Y.100, A:A.101, A:S.125, A:R.396 Water bridges: A:S.125 GOL.3: 8 residues within 4Å: Chain A: R.98, Q.99, Y.100, G.123, L.124, S.125, S.175 Ligands: GOL.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.98, A:Y.100, A:S.173 GOL.4: 5 residues within 4Å: Chain A: P.94, W.95, T.96, I.97, Q.403 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.95, A:I.97, A:I.97, A:Q.403 GOL.5: 5 residues within 4Å: Chain A: M.303, W.346, R.465, E.474, V.475 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.475, A:V.475 Water bridges: A:M.303, A:N.304, A:R.465 GOL.6: 6 residues within 4Å: Chain A: Q.208, R.218, Y.254, H.255, F.298 Ligands: B12.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.208, A:R.218 GOL.7: 6 residues within 4Å: Chain A: R.98, S.296, R.338, H.340, Q.373, S.374 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.96, A:R.98, A:R.98, A:S.374

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gouda, H. et al., Bivalent molecular mimicry by ADP protects metal redox state and promotes coenzyme B 12 repair. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-07-12

Peptides

Methylmalonyl-CoA mutase, mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Methylmalonyl-CoA mutase, mitochondrial

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