SMTL ID : 5imh.1

D31P mutant of C69-family cysteine dipeptidase from Lactobacillus farciminis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.47 Å

Oligo State

homo-pentamer

Ligands

7 x CO: COBALT (II) ION(Non-covalent)(Non-functional Binders)

CO.1: 1 residues within 4Å: Chain A: E.334 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.334 CO.2: 1 residues within 4Å: Chain A: D.201 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.201, H2O.3 CO.6: 2 residues within 4Å: Chain B: D.184, H.274 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.184, B:D.184, B:H.274 CO.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CO.9: 2 residues within 4Å: Chain C: D.184, H.274 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.184, C:D.184, C:H.274 CO.12: 1 residues within 4Å: Chain D: E.266 No protein-ligand interaction detected (PLIP) CO.13: 2 residues within 4Å: Chain E: K.16, D.183 No protein-ligand interaction detected (PLIP)

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

EDO.3: 6 residues within 4Å: Chain A: R.411, N.415 Chain C: R.107, L.111, N.218, L.220 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:N.218, A:N.415 Water bridges: A:R.411 EDO.4: 3 residues within 4Å: Chain A: P.182, D.184, H.274 No protein-ligand interaction detected (PLIP) EDO.5: 2 residues within 4Å: Chain A: N.330 Chain C: N.217 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:N.217, A:N.330 EDO.10: 4 residues within 4Å: Chain C: D.21, R.328, R.411, Q.414 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.328, C:R.411, C:R.411 EDO.11: 7 residues within 4Å: Chain C: S.256, P.257, D.258, D.259, H.274, A.275, N.276 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.258, C:N.276

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 3 residues within 4Å: Chain B: E.266, D.268 Chain E: D.258 No protein-ligand interaction detected (PLIP)

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