SMTL ID : 8gqb.1

Crystal structure of lasso peptide epimerase MslH D11A mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-octamer

Ligands

8 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: E.44, N.87, H.88, 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.5: 5 residues within 4Å: Chain B: E.44, N.87, H.88, 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.5, H2O.9 CA.9: 5 residues within 4Å: Chain C: E.44, N.87, H.88, 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.10, H2O.14 CA.13: 5 residues within 4Å: Chain D: E.44, N.87, H.88, 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.15, H2O.18 CA.17: 5 residues within 4Å: Chain E: E.44, N.87, H.88, 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.20, H2O.23 CA.21: 5 residues within 4Å: Chain F: E.44, N.87, H.88, 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.25, H2O.28 CA.25: 5 residues within 4Å: Chain G: E.44, N.87, H.88, 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.30, H2O.33 CA.29: 5 residues within 4Å: Chain H: E.44, N.87, H.88, 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.35, H2O.38

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: G.17, D.67, A.69 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.17, A:D.67 Water bridges: A:A.69, A:E.73 GOL.6: 3 residues within 4Å: Chain B: G.17, D.67, A.69 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.17, B:D.67 Water bridges: B:A.69, B:E.73 GOL.10: 3 residues within 4Å: Chain C: G.17, D.67, A.69 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.17, C:D.67 Water bridges: C:A.69, C:E.73 GOL.14: 3 residues within 4Å: Chain D: G.17, D.67, A.69 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.17, D:D.67 Water bridges: D:A.69, D:E.73 GOL.18: 3 residues within 4Å: Chain E: G.17, D.67, A.69 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:G.17, E:D.67 Water bridges: E:A.69, E:E.73 GOL.22: 3 residues within 4Å: Chain F: G.17, D.67, A.69 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:G.17, F:D.67 Water bridges: F:A.69, F:E.73 GOL.26: 3 residues within 4Å: Chain G: G.17, D.67, A.69 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:G.17, G:D.67 Water bridges: G:A.69, G:E.73 GOL.30: 3 residues within 4Å: Chain H: G.17, D.67, A.69 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:G.17, H:D.67 Water bridges: H:A.69, H:E.73

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

PEG.3: 3 residues within 4Å: Chain A: I.282, D.283, R.304 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.248 PEG.7: 3 residues within 4Å: Chain B: I.282, D.283, R.304 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.248 PEG.11: 3 residues within 4Å: Chain C: I.282, D.283, R.304 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.248 PEG.15: 3 residues within 4Å: Chain D: I.282, D.283, R.304 1 PLIP interactions: 1 interactions with chain D Water bridges: D:R.248 PEG.19: 3 residues within 4Å: Chain E: I.282, D.283, R.304 1 PLIP interactions: 1 interactions with chain E Water bridges: E:R.248 PEG.23: 3 residues within 4Å: Chain F: I.282, D.283, R.304 1 PLIP interactions: 1 interactions with chain F Water bridges: F:R.248 PEG.27: 3 residues within 4Å: Chain G: I.282, D.283, R.304 1 PLIP interactions: 1 interactions with chain G Water bridges: G:R.248 PEG.31: 3 residues within 4Å: Chain H: I.282, D.283, R.304 1 PLIP interactions: 1 interactions with chain H Water bridges: H:R.248

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

TRS.4: 4 residues within 4Å: Chain A: R.360, K.409, D.413, Q.416 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.409, A:D.413, A:Q.416, A:Q.416 TRS.8: 4 residues within 4Å: Chain B: R.360, K.409, D.413, Q.416 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.409, B:D.413, B:Q.416, B:Q.416 TRS.12: 4 residues within 4Å: Chain C: R.360, K.409, D.413, Q.416 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.409, C:D.413, C:Q.416, C:Q.416 TRS.16: 4 residues within 4Å: Chain D: R.360, K.409, D.413, Q.416 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.409, D:D.413, D:Q.416, D:Q.416 TRS.20: 4 residues within 4Å: Chain E: R.360, K.409, D.413, Q.416 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:K.409, E:D.413, E:Q.416, E:Q.416 TRS.24: 4 residues within 4Å: Chain F: R.360, K.409, D.413, Q.416 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:K.409, F:D.413, F:Q.416, F:Q.416 TRS.28: 4 residues within 4Å: Chain G: R.360, K.409, D.413, Q.416 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:K.409, G:D.413, G:Q.416, G:Q.416 TRS.32: 4 residues within 4Å: Chain H: R.360, K.409, D.413, Q.416 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:K.409, H:D.413, H:Q.416, 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)