SMTL ID : 6wfh.1

Streptomyces coelicolor methylmalonyl-CoA epimerase substrate complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 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: V0V.2 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: V0V.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.7, B:H.84, B:E.134

2 x V0V: (3S,5R,9R,19E)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9,19-tetrahydroxy-8,8,20-trimethyl-10,14-dioxo-2,4,6-trioxa-18-thia-11,15-diaza-3,5-diphosphahenicos-19-en-21-oic acid 3,5-dioxide (non-preferred name)(Non-covalent)

V0V.2: 23 residues within 4Å: Chain A: H.7, N.36, Q.39, E.43, Q.60, A.70, V.71, K.73, W.74, 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: CO.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.122 Hydrogen bonds: A:Q.39, A:Q.60, A:H.83, A:S.115, A:L.132 Water bridges: A:A.70, A:S.118 Salt bridges: A:H.7, A:K.73, A:K.73, A:K.126 V0V.8: 23 residues within 4Å: Chain B: H.7, N.36, Q.39, E.43, Q.60, A.70, V.71, K.73, W.74, 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: CO.7 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.122 Hydrogen bonds: B:Q.39, B:Q.60, B:H.83, B:S.115, B:L.132 Water bridges: B:A.70, B:S.118 Salt bridges: B:H.7, B:K.73, B:K.73, B:K.126

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

SO4.3: 3 residues within 4Å: Chain A: H.13, G.79, E.80 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.80, A:E.80, A:E.80 Salt bridges: A:H.13 SO4.9: 3 residues within 4Å: Chain B: H.13, G.79, E.80 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.80, B:E.80 Salt bridges: B:H.13

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

PEG.4: 6 residues within 4Å: Chain A: D.98, K.102 Chain B: R.23, A.24, G.27 Ligands: PEG.5 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.98, A:K.102, B:R.23 PEG.5: 4 residues within 4Å: Chain A: D.98, D.101, K.102 Ligands: PEG.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.98, A:K.102 PEG.10: 6 residues within 4Å: Chain A: R.23, A.24, G.27 Chain B: D.98, K.102 Ligands: PEG.11 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.98, B:K.102, A:R.23 PEG.11: 4 residues within 4Å: Chain B: D.98, D.101, K.102 Ligands: PEG.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.98, B:K.102

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

CL.6: 4 residues within 4Å: Chain A: V.35, N.36, E.37, R.113 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain B: V.35, N.36, E.37, R.113 Ligand excluded by PLIP

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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