SMTL ID : 6wf7.1

Methylmalonyl-CoA epimerase in complex with methylmalonyl-CoA and NH4+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

2 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.1: 6 residues within 4Å: Chain A: H.7, Q.60, H.84, E.134 Ligands: MC0.4, MCA.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.7, A:Q.60 NH4.6: 6 residues within 4Å: Chain B: H.7, Q.60, H.84, E.134 Ligands: MC0.9, MCA.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.60, B:E.134

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: H.13, G.79, E.80 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.80 Water bridges: A:G.79, A:E.80, A:E.80 Salt bridges: A:H.13 SO4.3: 7 residues within 4Å: Chain A: D.50, T.51, S.52 Chain B: D.50, T.51, S.52 Ligands: SO4.8 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:T.51, A:G.54 SO4.7: 3 residues within 4Å: Chain B: H.13, G.79, E.80 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.80 Water bridges: B:G.79, B:E.80 Salt bridges: B:H.13 SO4.8: 7 residues within 4Å: Chain A: D.50, T.51, S.52 Chain B: D.50, T.51, S.52 Ligands: SO4.3 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:G.54, A:T.51

2 x MC0: (S)-Methylmalonyl-Coenzyme A(Non-covalent)

MC0.4: 25 residues within 4Å: Chain A: H.7, N.36, Q.39, E.43, Q.60, A.70, V.71, K.73, W.74, K.77, H.83, H.84, L.107, Y.108, G.114, S.115, I.120, F.122, P.125, K.126, G.130, L.132, E.134 Ligands: NH4.1, MCA.5 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Q.39, A:I.120, A:F.122 Hydrogen bonds: A:Q.39, A:Q.60, A:K.77, A:H.83, A:S.115, A:L.132, A:E.134 Water bridges: A:N.36, A:W.74, A:K.77 Salt bridges: A:H.7, A:K.73, A:K.73, A:K.77, A:K.126 MC0.9: 25 residues within 4Å: Chain B: H.7, N.36, Q.39, E.43, Q.60, A.70, V.71, K.73, W.74, K.77, H.83, H.84, L.107, Y.108, G.114, S.115, I.120, F.122, P.125, K.126, G.130, L.132, E.134 Ligands: NH4.6, MCA.10 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Q.39, B:I.120, B:F.122 Hydrogen bonds: B:Q.39, B:Q.60, B:K.77, B:H.83, B:S.115, B:L.132, B:E.134 Water bridges: B:N.36, B:W.74, B:K.77 Salt bridges: B:H.7, B:K.73, B:K.73, B:K.77, B:K.126

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

MCA.5: 24 residues within 4Å: Chain A: H.7, Q.39, E.43, Q.60, A.70, V.71, K.73, W.74, K.77, H.83, H.84, L.107, Y.108, G.114, S.115, I.120, F.122, P.125, K.126, G.130, L.132, E.134 Ligands: NH4.1, MC0.4 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Q.39, A:I.120, A:F.122 Hydrogen bonds: A:Q.39, A:E.43, A:Q.60, A:K.77, A:H.83, A:S.115, A:L.132 Water bridges: A:N.36, A:W.74, A:K.77, A:S.118 Salt bridges: A:H.7, A:K.73, A:K.73, A:K.77, A:K.126 MCA.10: 24 residues within 4Å: Chain B: H.7, Q.39, E.43, Q.60, A.70, V.71, K.73, W.74, K.77, H.83, H.84, L.107, Y.108, G.114, S.115, I.120, F.122, P.125, K.126, G.130, L.132, E.134 Ligands: NH4.6, MC0.9 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:Q.39, B:I.120, B:F.122 Hydrogen bonds: B:Q.39, B:E.43, B:Q.60, B:K.77, B:H.83, B:S.115, B:L.132 Water bridges: B:N.36, B:W.74, B:K.77, B:S.118 Salt bridges: B:H.7, B:K.73, B:K.73, B:K.77, B:K.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stunkard, L.M. et al., Substrate Enolate Intermediate and Mimic Captured in the Active Site of Streptomyces coelicolor Methylmalonyl-CoA Epimerase. Chembiochem (2022)

Release Date

2020-07-08

Peptides

Methylmalonyl-CoA epimerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Methylmalonyl-CoA epimerase

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