SMTL ID : 8gq9.1

Crystal structure of lasso peptide epimerase MslH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-octamer

Ligands

24 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: E.268, D.413, Q.416, L.417 Ligands: TRS.5 Ligand excluded by PLIP GOL.2: 3 residues within 4Å: Chain A: D.72, T.75, A.76 Ligand excluded by PLIP GOL.3: 2 residues within 4Å: Chain A: I.282, D.283 Ligand excluded by PLIP GOL.6: 5 residues within 4Å: Chain B: E.268, D.413, Q.416, L.417 Ligands: TRS.10 Ligand excluded by PLIP GOL.7: 3 residues within 4Å: Chain B: D.72, T.75, A.76 Ligand excluded by PLIP GOL.8: 2 residues within 4Å: Chain B: I.282, D.283 Ligand excluded by PLIP GOL.11: 5 residues within 4Å: Chain C: E.268, D.413, Q.416, L.417 Ligands: TRS.15 Ligand excluded by PLIP GOL.12: 3 residues within 4Å: Chain C: D.72, T.75, A.76 Ligand excluded by PLIP GOL.13: 2 residues within 4Å: Chain C: I.282, D.283 Ligand excluded by PLIP GOL.16: 5 residues within 4Å: Chain D: E.268, D.413, Q.416, L.417 Ligands: TRS.20 Ligand excluded by PLIP GOL.17: 3 residues within 4Å: Chain D: D.72, T.75, A.76 Ligand excluded by PLIP GOL.18: 2 residues within 4Å: Chain D: I.282, D.283 Ligand excluded by PLIP GOL.21: 5 residues within 4Å: Chain E: E.268, D.413, Q.416, L.417 Ligands: TRS.25 Ligand excluded by PLIP GOL.22: 3 residues within 4Å: Chain E: D.72, T.75, A.76 Ligand excluded by PLIP GOL.23: 2 residues within 4Å: Chain E: I.282, D.283 Ligand excluded by PLIP GOL.26: 5 residues within 4Å: Chain F: E.268, D.413, Q.416, L.417 Ligands: TRS.30 Ligand excluded by PLIP GOL.27: 3 residues within 4Å: Chain F: D.72, T.75, A.76 Ligand excluded by PLIP GOL.28: 2 residues within 4Å: Chain F: I.282, D.283 Ligand excluded by PLIP GOL.31: 5 residues within 4Å: Chain G: E.268, D.413, Q.416, L.417 Ligands: TRS.35 Ligand excluded by PLIP GOL.32: 3 residues within 4Å: Chain G: D.72, T.75, A.76 Ligand excluded by PLIP GOL.33: 2 residues within 4Å: Chain G: I.282, D.283 Ligand excluded by PLIP GOL.36: 5 residues within 4Å: Chain H: E.268, D.413, Q.416, L.417 Ligands: TRS.40 Ligand excluded by PLIP GOL.37: 3 residues within 4Å: Chain H: D.72, T.75, A.76 Ligand excluded by PLIP GOL.38: 2 residues within 4Å: Chain H: I.282, D.283 Ligand excluded by PLIP

8 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: E.44, N.87, H.259, H.261 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.44, A:H.259, A:H.261, H2O.1, H2O.4 CA.9: 4 residues within 4Å: Chain B: E.44, N.87, H.259, H.261 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.44, B:H.259, B:H.261, H2O.8, H2O.12 CA.14: 4 residues within 4Å: Chain C: E.44, N.87, H.259, H.261 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.44, C:H.259, C:H.261, H2O.16, H2O.20 CA.19: 4 residues within 4Å: Chain D: E.44, N.87, H.259, H.261 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.44, D:H.259, D:H.261, H2O.24, H2O.28 CA.24: 4 residues within 4Å: Chain E: E.44, N.87, H.259, H.261 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.44, E:H.259, E:H.261, H2O.32, H2O.36 CA.29: 4 residues within 4Å: Chain F: E.44, N.87, H.259, H.261 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.44, F:H.259, F:H.261, H2O.40, H2O.43 CA.34: 4 residues within 4Å: Chain G: E.44, N.87, H.259, H.261 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.44, G:H.259, G:H.261, H2O.47, H2O.51 CA.39: 4 residues within 4Å: Chain H: E.44, N.87, H.259, H.261 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.44, H:H.259, H:H.261, H2O.55, H2O.59

8 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.5: 5 residues within 4Å: Chain A: K.409, T.412, D.413, Q.416 Ligands: GOL.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.409, A:Q.416 Water bridges: A:T.412 TRS.10: 5 residues within 4Å: Chain B: K.409, T.412, D.413, Q.416 Ligands: GOL.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.409, B:Q.416 Water bridges: B:T.412 TRS.15: 5 residues within 4Å: Chain C: K.409, T.412, D.413, Q.416 Ligands: GOL.11 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.409, C:Q.416 Water bridges: C:T.412 TRS.20: 5 residues within 4Å: Chain D: K.409, T.412, D.413, Q.416 Ligands: GOL.16 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.409, D:Q.416 Water bridges: D:T.412 TRS.25: 5 residues within 4Å: Chain E: K.409, T.412, D.413, Q.416 Ligands: GOL.21 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.409, E:Q.416 TRS.30: 5 residues within 4Å: Chain F: K.409, T.412, D.413, Q.416 Ligands: GOL.26 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.409, F:Q.416 TRS.35: 5 residues within 4Å: Chain G: K.409, T.412, D.413, Q.416 Ligands: GOL.31 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:K.409, G:Q.416 TRS.40: 5 residues within 4Å: Chain H: K.409, T.412, D.413, Q.416 Ligands: GOL.36 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:K.409, H:Q.416

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakashima, Y. et al., Structure of lasso peptide epimerase MslH reveals metal-dependent acid/base catalytic mechanism. Nat Commun (2023)

Release Date

2023-06-21

Peptides

Poly-gamma-glutamate synthesis protein (Capsule biosynthesis protein): ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

Poly-gamma-glutamate synthesis protein (Capsule biosynthesis protein)

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