SMTL ID : 6oxd.1

Structure of Mycobacterium tuberculosis methylmalonyl-CoA mutase with adenosyl cobalamin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-mer

Ligands

1 x B12: COBALAMIN(Non-covalent)

B12.1: 58 residues within 4Å: Chain A: Y.105, A.132, F.133, L.135, H.138, A.155, G.156, V.222, R.223, N.224, T.225, Y.259, H.260, E.263, A.264, G.349, W.350, L.352, D.385, E.386, A.387, L.388, A.389, L.390, P.391, K.459, Q.470, I.619, I.621, D.627, G.628, H.629, D.630, R.631, G.632, V.635, I.636, F.640, G.672, V.673, S.674, L.676, A.677, A.678, V.702, G.704, G.705, V.706, F.724, P.725, P.726, G.727, T.728, I.730, A.733, L.737 Ligands: 5AD.2, NJS.3 38 PLIP interactions: 38 interactions with chain A, Hydrophobic interactions: A:L.135, A:R.223, A:Y.259, A:H.260, A:E.386, A:L.390, A:I.619, A:V.635, A:I.636, A:F.640, A:F.724, A:F.724 Hydrogen bonds: A:Y.105, A:F.133, A:R.223, A:R.223, A:G.349, A:E.386, A:Q.470, A:D.627, A:G.628, A:H.629, A:D.630, A:D.630, A:R.631, A:G.632, A:S.674, A:L.676, A:G.705, A:F.724, A:G.727, A:T.728, A:T.728 Water bridges: A:F.133, A:L.390, A:A.678, A:A.678 Metal complexes: A:H.629

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

5AD.2: 17 residues within 4Å: Chain A: Y.105, A.106, G.107, F.108, A.132, A.155, G.156, Y.259, Q.346, G.349, H.380, N.382, E.386, L.390, P.391 Ligands: B12.1, NJS.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.107, A:A.155, A:Q.346, A:E.386, A:E.386 Water bridges: A:Y.259, A:H.380

1 x NJS: Itaconyl coenzyme A(Non-covalent)

NJS.3: 29 residues within 4Å: Chain A: Y.91, T.93, M.94, N.97, Q.98, T.101, R.103, Y.105, S.130, S.180, T.182, T.211, Q.213, R.223, N.252, Y.259, H.260, R.299, S.301, F.303, R.342, T.343, H.344, Q.346, Q.377, S.378 Chain B: V.26 Ligands: B12.1, 5AD.2 37 PLIP interactions: 37 interactions with chain A Hydrophobic interactions: A:Y.105, A:Y.259, A:H.344 Hydrogen bonds: A:Y.91, A:T.93, A:T.93, A:N.97, A:Q.98, A:T.101, A:R.103, A:R.103, A:Y.105, A:S.130, A:S.130, A:S.178, A:T.182, A:T.211, A:Q.213, A:H.260 Water bridges: A:S.178, A:S.178, A:S.180, A:N.252, A:N.252, A:R.299, A:R.299, A:R.342, A:R.342, A:R.342, A:R.342, A:R.342, A:H.344, A:H.344 Salt bridges: A:R.103, A:R.223, A:H.260, A:R.299

1 x K: POTASSIUM ION(Non-covalent)

K.4: 7 residues within 4Å: Chain A: A.136, T.137, Y.141, D.142, S.143, I.159, D.160 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.141, A:I.159, A:D.160, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruetz, M. et al., Itaconyl-CoA forms a stable biradical in methylmalonyl-CoA mutase and derails its activity and repair. Science (2019)

Release Date

2019-11-13

Peptides

Methylmalonyl-CoA mutase large subunit: A
Methylmalonyl-CoA mutase small subunit: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Methylmalonyl-CoA mutase large subunit

Methylmalonyl-CoA mutase small subunit

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