SMTL ID : 5inx.1

A C69-family cysteine dipeptidase in complex with Met and Ala from Lactobacillus farciminis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-pentamer

Ligands

5 x MET: METHIONINE(Non-covalent)(Covalent)

MET.1: 10 residues within 4Å: Chain A: C.9, R.28, D.30, D.31, T.99, E.100, T.101, E.121, N.191 Ligands: ALA.2 9 PLIP interactions: 7 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:C.9, A:D.30, A:T.99, A:T.99, A:T.99, A:T.101, A:N.191, A.2 Hydrophobic interactions: A.2 MET.3: 10 residues within 4Å: Chain B: C.9, R.28, D.30, D.31, T.99, E.100, T.101, E.121, N.191 Ligands: ALA.4 9 PLIP interactions: 7 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:C.9, B:D.30, B:T.99, B:T.99, B:T.99, B:T.101, B:N.191, A.4 Hydrophobic interactions: A.4 MET.5: 10 residues within 4Å: Chain C: C.9, R.28, D.30, D.31, T.99, E.100, T.101, E.121, N.191 Ligands: ALA.6 7 PLIP interactions: 5 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: C:C.9, C:T.99, C:T.101, C:N.191, A.6 Water bridges: C:R.28 Hydrophobic interactions: A.6 MET.7: 8 residues within 4Å: Chain D: C.9, R.28, T.99, E.100, T.101, E.121, N.191 Ligands: ALA.8 6 PLIP interactions: 5 interactions with chain D, 1 Ligand-Ligand interactions Hydrogen bonds: D:T.99, D:T.99, D:T.99, D:T.101, D:N.191 Hydrophobic interactions: A.8 MET.9: 8 residues within 4Å: Chain E: C.9, R.28, T.99, E.100, T.101, E.121, N.191 Ligands: ALA.10 7 PLIP interactions: 5 interactions with chain E, 2 Ligand-Ligand interactions Hydrogen bonds: E:C.9, E:T.99, E:T.99, E:T.101, E:N.191, A.10 Hydrophobic interactions: A.10

5 x ALA: ALANINE(Non-covalent)

ALA.2: 7 residues within 4Å: Chain A: C.9, D.31, N.191, Y.243, R.312, R.318 Ligands: MET.1 6 PLIP interactions: 1 Ligand-Ligand interactions, 5 interactions with chain A Hydrophobic interactions: M.1 Hydrogen bonds: A:C.9, A:C.9, A:N.191 Salt bridges: A:R.312, A:R.318 ALA.4: 8 residues within 4Å: Chain B: C.9, D.31, T.101, N.191, Y.243, R.312, R.318 Ligands: MET.3 8 PLIP interactions: 2 Ligand-Ligand interactions, 6 interactions with chain B Hydrophobic interactions: M.3 Hydrogen bonds: A.4, B:C.9, B:C.9, B:C.9, B:N.191 Salt bridges: B:R.312, B:R.318 ALA.6: 7 residues within 4Å: Chain C: C.9, D.31, N.191, Y.243, R.312, R.318 Ligands: MET.5 6 PLIP interactions: 5 interactions with chain C, 1 Ligand-Ligand interactions Hydrogen bonds: C:C.9, C:C.9, C:N.191 Salt bridges: C:R.312, C:R.318 Hydrophobic interactions: M.5 ALA.8: 8 residues within 4Å: Chain D: C.9, D.31, T.101, N.191, Y.243, R.312, R.318 Ligands: MET.7 7 PLIP interactions: 2 Ligand-Ligand interactions, 5 interactions with chain D Hydrophobic interactions: M.7 Hydrogen bonds: A.8, D:C.9, D:C.9, D:C.9 Salt bridges: D:R.312, D:R.318 ALA.10: 8 residues within 4Å: Chain E: C.9, D.31, T.101, N.191, Y.243, R.312, R.318 Ligands: MET.9 7 PLIP interactions: 3 Ligand-Ligand interactions, 4 interactions with chain E Hydrophobic interactions: M.9 Hydrogen bonds: A.10, A.10, E:C.9, E:C.9 Salt bridges: E:R.312, E:R.318

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kono, R. et al., A C69-family cysteine dipeptidase from Lactobacillus farciminis; substrate recognition mechanism and autoproteolytic mechanism in enzyme maturation. To Be Published

Release Date

2017-03-15

Peptides

Dipeptidase: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Dipeptidase

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