SMTL ID : 5img.1 (1 other biounit)

C9A mutant of C69-family cysteine dipeptidase from Lactobacillus farciminis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-pentamer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain C: I.5, K.6, G.32, H.33, D.37, N.76, W.84, H.320 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:K.6, C:H.33, C:D.37, C:N.76, C:W.84 Water bridges: C:E.34 GOL.2: 5 residues within 4Å: Chain B: P.257, D.258, N.276 Chain C: E.266, D.268 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:N.276, C:E.266, C:D.268 Water bridges: B:N.276, C:D.268, C:D.268 GOL.6: 8 residues within 4Å: Chain E: I.5, K.6, G.32, H.33, D.37, N.76, W.84, H.320 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:K.6, E:H.33, E:N.76, E:H.320 Water bridges: E:K.6, E:E.34, E:E.34, E:Q.39

4 x CO: COBALT (II) ION(Non-covalent)

CO.3: 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.4: 1 residues within 4Å: Chain C: D.66 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.66, H2O.51, H2O.63 CO.5: 1 residues within 4Å: Chain D: E.428 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.428, H2O.80, H2O.81 CO.7: 2 residues within 4Å: Chain E: D.203, D.204 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.203, E:D.204, H2O.111

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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