SMTL ID : 8itg.1

Crystal structure of lasso peptide epimerase MslH in complexed with precursor peptide variant MslAW21G

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-8-8-mer

Ligands

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

TRS.1: 2 residues within 4Å: Chain A: R.404, E.408 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.404 TRS.3: 2 residues within 4Å: Chain C: R.404, E.408 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.404 TRS.5: 2 residues within 4Å: Chain E: R.404, E.408 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.404 TRS.7: 2 residues within 4Å: Chain G: R.404, E.408 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:R.404 TRS.9: 2 residues within 4Å: Chain I: R.404, E.408 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:R.404 TRS.11: 2 residues within 4Å: Chain K: R.404, E.408 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:R.404 TRS.13: 2 residues within 4Å: Chain M: R.404, E.408 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:R.404 TRS.15: 2 residues within 4Å: Chain O: R.404, E.408 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:R.404

8 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: E.44, N.87, H.259, H.261 Chain B: G.42 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:E.44, A:H.259, A:H.261, B:G.42, H2O.1 CA.4: 5 residues within 4Å: Chain C: E.44, N.87, H.259, H.261 Chain D: G.42 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: C:E.44, C:H.259, C:H.261, D:G.42, H2O.9 CA.6: 5 residues within 4Å: Chain E: E.44, N.87, H.259, H.261 Chain F: G.42 5 PLIP interactions: 1 interactions with chain F, 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: F:G.42, E:E.44, E:H.259, E:H.261, H2O.18 CA.8: 5 residues within 4Å: Chain G: E.44, N.87, H.259, H.261 Chain H: G.42 5 PLIP interactions: 3 interactions with chain G, 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: G:E.44, G:H.259, G:H.261, H:G.42, H2O.26 CA.10: 5 residues within 4Å: Chain I: E.44, N.87, H.259, H.261 Chain J: G.42 5 PLIP interactions: 3 interactions with chain I, 1 interactions with chain J, 1 Ligand-Water interactions Metal complexes: I:E.44, I:H.259, I:H.261, J:G.42, H2O.34 CA.12: 5 residues within 4Å: Chain K: E.44, N.87, H.259, H.261 Chain L: G.42 5 PLIP interactions: 3 interactions with chain K, 1 interactions with chain L, 1 Ligand-Water interactions Metal complexes: K:E.44, K:H.259, K:H.261, L:G.42, H2O.42 CA.14: 5 residues within 4Å: Chain M: E.44, N.87, H.259, H.261 Chain N: G.42 5 PLIP interactions: 3 interactions with chain M, 1 interactions with chain N, 1 Ligand-Water interactions Metal complexes: M:E.44, M:H.259, M:H.261, N:G.42, H2O.51 CA.16: 5 residues within 4Å: Chain O: E.44, N.87, H.259, H.261 Chain P: G.42 5 PLIP interactions: 1 interactions with chain P, 3 interactions with chain O, 1 Ligand-Water interactions Metal complexes: P:G.42, O:E.44, O:H.259, O:H.261, H2O.59

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): ACEGIKMO
Tricyclic peptide MS-271: BDFHJLNP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

G
A

I
A

K
A

M
A

O
A

B
B

D
B

F
B

H
B

J
B

L
B

N
B

P
B

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

Tricyclic peptide MS-271

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