SMTL ID : 6wfi.1

Methylmalonyl-CoA epimerase in complex with 2-nitronate-propionyl-CoA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.37 Å

Oligo State

homo-dimer

Ligands

2 x CO: COBALT (II) ION(Non-covalent)

CO.1: 5 residues within 4Å: Chain A: H.7, Q.60, H.84, E.134 Ligands: KFV.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.7, A:H.84, A:E.134 CO.7: 5 residues within 4Å: Chain B: H.7, Q.60, H.84, E.134 Ligands: KFV.12 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.7, B:H.84, 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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.80 Water bridges: A:G.79, A:E.80, A:E.80, A:E.80, A:E.80 Salt bridges: A:H.13 SO4.3: 3 residues within 4Å: Chain A: R.23, A.24 Chain B: K.102 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Water bridges: B:K.102, B:K.102, A:R.23 Salt bridges: B:K.102, A:R.23 SO4.8: 3 residues within 4Å: Chain B: H.13, G.79, E.80 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.80 Water bridges: B:G.79, B:E.80, B:E.80 Salt bridges: B:H.13 SO4.9: 3 residues within 4Å: Chain A: K.102 Chain B: R.23, A.24 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Water bridges: A:K.102, A:K.102, B:R.23 Salt bridges: A:K.102, B:R.23

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: V.35, N.36, E.37, R.113 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: V.35, N.36, E.37, R.113 Ligand excluded by PLIP

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 3 residues within 4Å: Chain A: R.105, H.124, K.126 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.105, A:R.105, A:K.126 Water bridges: A:D.127 PEG.11: 3 residues within 4Å: Chain B: R.105, H.124, K.126 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.105, B:R.105, B:K.126

2 x KFV: [1-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-1-oxidanylidene-propan-2-ylidene]-bis(oxidanidyl)azanium(Non-covalent)

KFV.6: 23 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, G.130, L.132, E.134 Ligands: CO.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.107, A:F.122 Hydrogen bonds: A:Q.39, A:K.77, A:H.83, A:L.132 Water bridges: A:K.73, A:K.73, A:N.78 Salt bridges: A:K.73, A:K.73, A:K.126 KFV.12: 23 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, G.130, L.132, E.134 Ligands: CO.7 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.107, B:F.122 Hydrogen bonds: B:Q.39, B:K.77, B:H.83, B:L.132 Water bridges: B:K.73, B:K.73, B:N.78, B:Y.108 Salt bridges: B:K.73, B:K.73, 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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