SMTL ID : 8dyj.1

Crystal structure of human methylmalonyl-CoA mutase in complex with ADP and cob(II)alamin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x B12: COBALAMIN(Non-covalent)

B12.1: 40 residues within 4Å: Chain A: Y.100, F.128, L.130, H.133, A.150, V.217, R.218, T.220, Y.254, H.255, E.258, G.345, W.346, L.348, E.382, A.383, G.385, L.386, Q.466, D.615, G.616, H.617, D.618, R.619, G.620, I.624, 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: ADP.2 39 PLIP interactions: 39 interactions with chain A, Hydrophobic interactions: A:L.130, A:V.217, A:R.218, A:Y.254, A:H.255, A:E.382, A:L.386, A:I.624, A:L.664, A:L.664, A:V.694, A:V.694, A:F.712, A:F.712 Hydrogen bonds: A:F.128, A:R.218, A:R.218, A:G.345, A:E.382, A:Q.466, A:G.616, A:H.617, A:D.618, A:D.618, A:R.619, A:G.620, A:L.664, A:G.693, A:T.716 Water bridges: A:F.128, A:F.128, A:L.386, A:A.666, A:A.666, A:G.715, A:G.715, A:G.715 pi-Stacking: A:H.617 Metal complexes: A:H.617

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 17 residues within 4Å: Chain A: Y.100, A.101, G.102, A.127, A.150, T.177, Q.208, R.218, Y.254, H.255, F.298, Q.342, N.378, E.382, L.386, P.387 Ligands: B12.1 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.102, A:A.150, A:Q.208, A:Q.208, A:Q.342, A:E.382 Salt bridges: A:R.218, A:H.255, A:H.255 pi-Stacking: A:Y.100, A:Y.100

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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