SMTL ID : 5od9.1

Structure of the engineered metalloesterase MID1sc9

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.13 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.41, E.60, H.63 Chain B: H.67 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Metal complexes: B:H.67, A:H.41, A:E.60, A:E.60, A:H.63 ZN.2: 4 residues within 4Å: Chain A: H.37, H.63, H.67 Ligands: CL.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.37, A:H.63, A:H.67 ZN.11: 4 residues within 4Å: Chain A: H.67 Chain B: H.37, H.41 Ligands: CL.4 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Metal complexes: A:H.67, B:H.37, B:H.41 ZN.12: 5 residues within 4Å: Chain A: H.37, H.41 Chain B: E.34, H.37 Ligands: CL.13 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Metal complexes: B:E.34, B:E.34, B:H.37, A:H.37

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

CL.3: 6 residues within 4Å: Chain A: Q.33, E.34, H.37, H.63, H.67 Ligands: ZN.2 Ligand excluded by PLIP CL.4: 7 residues within 4Å: Chain A: H.67 Chain B: H.37, H.41, H.63, V.64, H.67 Ligands: ZN.11 Ligand excluded by PLIP CL.13: 8 residues within 4Å: Chain A: H.37, H.41 Chain B: E.34, H.37, I.66, H.67, R.70 Ligands: ZN.12 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 2 residues within 4Å: Chain A: E.91, Q.94 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.91, H2O.1, H2O.2, H2O.3 MG.6: 1 residues within 4Å: Chain A: N.12 No protein-ligand interaction detected (PLIP)

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 6 residues within 4Å: Chain A: I.17, Q.33, I.66, S.82, T.85, L.86 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.33, A:S.82, A:L.86 EDO.8: 1 residues within 4Å: Chain A: E.42 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.9

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.9: 6 residues within 4Å: Chain A: P.38, E.42, Q.45 Chain B: T.31, E.34, R.70 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Water bridges: B:T.31, B:R.70, A:E.42, A:Q.45, A:Q.45, A:Q.45

1 x 9RW: (2~{S})-2-phenylpropanoic acid(Non-covalent)

9RW.10: 6 residues within 4Å: Chain A: Q.58, G.62, L.65, R.80, L.81, N.84 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.65, A:L.81, A:N.84 Hydrogen bonds: A:N.84 Water bridges: A:R.80 Salt bridges: A:R.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Studer, S. et al., Evolution of a highly active and enantiospecific metalloenzyme from short peptides. Science (2018)

Release Date

2018-12-12

Peptides

MID1sc9: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

MID1sc9