SMTL ID : 2xiq.3 (2 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x B12: COBALAMIN(Non-covalent)

B12.1: 41 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, F.628, G.660, S.662, L.664, A.665, A.666, G.692, G.693, V.694, F.712, G.713, P.714, T.716 Ligands: 5AD.2, MLC.3 36 PLIP interactions: 36 interactions with chain A, Hydrophobic interactions: A:L.130, A:R.218, A:Y.254, A:E.382, A:L.386, A:I.624, A:I.624, A:F.628, A:V.694, A:V.694, A:F.712, A:F.712 Hydrogen bonds: A:Y.100, A:F.128, A:H.133, A:R.218, A:R.218, A:G.345, A:L.386, A:D.615, A:G.616, A:H.617, A:D.618, A:D.618, A:D.618, A:R.619, A:G.620, A:L.664, A:G.693, A:G.715, A:T.716 Water bridges: A:N.219, A:Q.466, A:A.666, A:A.666 Metal complexes: A:H.617 B12.4: 45 residues within 4Å: Chain B: Y.100, A.127, F.128, L.130, H.133, A.150, V.217, R.218, T.220, Y.254, H.255, E.258, A.259, 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, V.623, 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: 5AD.5, MLC.6 35 PLIP interactions: 35 interactions with chain B, Hydrophobic interactions: B:L.130, B:R.218, B:Y.254, B:H.255, B:A.259, B:E.382, B:L.386, B:V.623, B:I.624, B:I.624, B:F.628, B:V.694, B:V.694, B:F.712, B:F.712 Hydrogen bonds: B:F.128, B:H.133, B:R.218, B:R.218, B:G.345, B:L.386, B:Q.466, B:G.616, B:H.617, B:D.618, B:D.618, B:R.619, B:G.620, B:L.664, B:G.693, B:G.715, B:T.716 Water bridges: B:Y.100, B:Y.100 Metal complexes: B:H.617

2 x 5AD: 5'-DEOXYADENOSINE(Non-covalent)

5AD.2: 13 residues within 4Å: Chain A: Y.100, G.102, A.150, Y.254, Q.342, G.345, H.376, N.378, E.382, L.386, P.387 Ligands: B12.1, MLC.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.254 Hydrogen bonds: A:G.102, A:G.102, A:Y.254, A:Q.342, A:E.382 Water bridges: A:H.376, A:S.379 pi-Stacking: A:Y.100, A:Y.100 5AD.5: 13 residues within 4Å: Chain B: Y.100, A.101, G.102, A.127, Y.254, Q.342, G.345, N.378, E.382, L.386, P.387 Ligands: B12.4, MLC.6 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.102, B:G.102, B:Q.342, B:N.378, B:E.382 Water bridges: B:S.379 pi-Stacking: B:Y.100, B:Y.100

2 x MLC: MALONYL-COENZYME A(Non-covalent)

MLC.3: 29 residues within 4Å: Chain A: Y.86, T.88, M.89, F.92, R.93, T.96, R.98, Y.100, S.125, S.175, T.177, T.206, Q.208, R.218, K.245, N.247, H.255, R.294, S.296, F.298, R.338, A.339, H.340, Q.342, Q.373, S.374 Chain B: Q.40 Ligands: B12.1, 5AD.2 42 PLIP interactions: 41 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.100, A:R.338, A:H.340 Hydrogen bonds: A:Y.86, A:Y.86, A:T.88, A:T.88, A:T.96, A:T.96, A:R.98, A:Y.100, A:S.125, A:S.175, A:T.177, A:T.206, A:Q.208, A:S.296, A:S.296, A:S.374, B:Q.40 Water bridges: A:Y.86, A:R.93, A:R.93, A:R.93, A:S.173, A:S.173, A:S.175, A:N.247, A:N.247, A:N.247, A:N.247, A:R.294, A:R.294, A:R.338, A:R.338 Salt bridges: A:R.93, A:R.93, A:R.98, A:R.218, A:K.245, A:H.255, A:R.294 MLC.6: 29 residues within 4Å: Chain A: Q.40 Chain B: Y.86, T.88, M.89, F.92, R.93, T.96, R.98, Y.100, S.125, S.175, T.177, T.206, Q.208, R.218, K.245, N.247, H.255, R.294, S.296, F.298, R.338, A.339, H.340, Q.342, Q.373, S.374 Ligands: B12.4, 5AD.5 41 PLIP interactions: 40 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.100, B:R.338, B:H.340 Hydrogen bonds: B:Y.86, B:Y.86, B:T.88, B:R.93, B:R.93, B:T.96, B:T.96, B:R.98, B:Y.100, B:S.125, B:S.175, B:Q.208, B:S.296, B:S.374 Water bridges: B:S.173, B:S.173, B:S.173, B:S.175, B:T.177, B:T.206, B:T.206, B:K.245, B:N.247, B:N.247, B:S.250, B:S.296, B:R.338, B:R.338, B:R.338, B:R.338, A:Q.40 Salt bridges: B:R.93, B:R.93, B:R.98, B:R.218, B:K.245, B:H.255, B:R.294

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Froese, D.S. et al., Structures of the Human Gtpase Mmaa and Vitamin B12-Dependent Methylmalonyl-Coa Mutase and Insight Into Their Complex Formation. J.Biol.Chem. (2010)

Release Date

2010-09-29

Peptides

METHYLMALONYL-COA MUTASE, MITOCHONDRIAL: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

METHYLMALONYL-COA MUTASE, MITOCHONDRIAL

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