SMTL ID : 4req.1 (1 other biounit)

Methylmalonyl-COA Mutase substrate complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-mer

Ligands

1 x B12: COBALAMIN(Non-covalent)

B12.1: 46 residues within 4Å: Chain A: Y.88, A.115, F.116, L.118, H.121, A.138, V.205, R.206, T.208, Y.242, H.243, E.246, G.332, W.333, L.335, E.369, A.370, A.372, L.373, Q.453, L.601, D.607, G.608, H.609, D.610, R.611, G.612, V.615, I.616, Y.620, G.652, S.654, L.656, A.657, G.658, G.684, G.685, V.686, Y.704, T.705, P.706, T.708, S.713 Ligands: SCA.2, MCA.3, 5AD.4 37 PLIP interactions: 37 interactions with chain A, Hydrophobic interactions: A:L.118, A:R.206, A:Y.242, A:H.243, A:L.373, A:L.601, A:V.615, A:I.616, A:I.616, A:V.686, A:Y.704, A:Y.704 Hydrogen bonds: A:F.116, A:R.206, A:G.332, A:E.369, A:Q.453, A:G.608, A:H.609, A:H.609, A:D.610, A:D.610, A:D.610, A:R.611, A:G.612, A:L.656, A:G.685, A:T.708, A:T.708 Water bridges: A:R.206, A:R.206, A:L.373, A:E.446, A:G.707, A:G.707, A:G.707 Metal complexes: A:H.609

1 x SCA: SUCCINYL-COENZYME A(Non-covalent)

SCA.2: 33 residues within 4Å: Chain A: Y.74, T.76, M.77, F.80, R.81, T.84, R.86, Y.88, S.113, S.161, S.163, T.165, T.194, Q.196, R.206, N.235, S.238, Y.242, H.243, R.282, S.284, F.286, R.325, T.326, H.327, Q.329, Q.360, S.361 Chain B: V.41, R.44 Ligands: B12.1, MCA.3, 5AD.4 41 PLIP interactions: 39 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.88, A:Y.242, A:R.325, A:H.327 Hydrogen bonds: A:Y.74, A:T.76, A:R.81, A:T.84, A:T.84, A:R.86, A:Y.88, A:S.113, A:S.161, A:S.163, A:Q.196, A:S.284, A:S.361, B:R.44, B:R.44 Water bridges: A:Y.74, A:Y.74, A:T.76, A:S.163, A:T.165, A:T.194, A:N.235, A:N.235, A:N.235, A:N.235, A:N.235, A:S.284, A:K.320, A:R.325, A:R.325 Salt bridges: A:R.86, A:R.206, A:H.243, A:R.282 pi-Stacking: A:Y.74, A:Y.74 pi-Cation interactions: A:R.81

1 x MCA: METHYLMALONYL-COENZYME A(Non-covalent)

MCA.3: 31 residues within 4Å: Chain A: Y.74, T.76, M.77, F.80, R.81, T.84, R.86, Y.88, S.113, S.163, T.165, T.194, Q.196, R.206, N.235, Y.242, H.243, R.282, S.284, F.286, R.325, T.326, H.327, Q.329, Q.360, S.361 Chain B: V.41, R.44 Ligands: B12.1, SCA.2, 5AD.4 42 PLIP interactions: 40 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.88, A:Y.242, A:H.327 Hydrogen bonds: A:Y.74, A:T.76, A:R.81, A:T.84, A:T.84, A:R.86, A:Y.88, A:S.113, A:S.163, A:Q.196, A:S.284, A:S.361, B:R.44, B:R.44 Water bridges: A:Y.74, A:T.76, A:S.161, A:S.161, A:S.161, A:S.163, A:T.165, A:T.194, A:N.235, A:N.235, A:N.235, A:N.235, A:R.282, A:S.284, A:K.320, A:R.325, A:R.325, A:R.325 Salt bridges: A:R.86, A:R.206, A:H.243, A:R.282 pi-Stacking: A:Y.74, A:Y.74 pi-Cation interactions: A:R.81

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

5AD.4: 14 residues within 4Å: Chain A: Y.88, A.89, G.90, A.115, A.138, G.139, Y.242, Q.329, N.365, E.369, L.373 Ligands: B12.1, SCA.2, MCA.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.88 Hydrogen bonds: A:G.90, A:G.90, A:Y.242, A:Q.329, A:H.363, A:E.369 Water bridges: A:S.366, A:E.369

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: A.40, E.41, T.250 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.41, A:E.296 Water bridges: A:M.291, A:N.292 GOL.6: 7 residues within 4Å: Chain B: F.92, T.96, D.315, K.316, R.317, G.318, R.320 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.315, B:K.316, B:G.318, B:R.320, B:R.320 Water bridges: B:R.320

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mancia, F. et al., Conformational changes on substrate binding to methylmalonyl CoA mutase and new insights into the free radical mechanism. Structure (1998)

Release Date

1999-01-13

Peptides

METHYLMALONYL-COA MUTASE: A
METHYLMALONYL-COA MUTASE: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

METHYLMALONYL-COA MUTASE

METHYLMALONYL-COA MUTASE

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