SMTL ID : 5inr.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-pentamer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: Y.300, D.391, Y.392, D.393 Ligand excluded by PLIP EDO.2: 3 residues within 4Å: Chain A: N.375, F.443, N.447 Ligand excluded by PLIP EDO.3: 3 residues within 4Å: Chain A: G.451, D.452, T.455 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: N.105, S.106 Chain B: E.403, L.404 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: A.236 Chain B: F.254, E.282, D.283, F.286 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: F.254, E.282, D.283, F.286 Chain E: A.236 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: N.105, R.107, R.230, H.231, G.234, S.235, A.236 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: R.70, I.89, N.90, S.91, A.356, N.357, V.358 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: F.372, D.373, L.374, N.375 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain B: Y.300, D.391, Y.392, D.393 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain B: N.105, S.106 Chain D: L.404 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain B: G.451, D.452, T.455 Ligand excluded by PLIP EDO.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain B: N.105, R.107, R.230, H.231, G.234, S.235, A.236 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain B: A.236, Q.267 Chain D: F.254 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain B: R.70, I.89, N.90, S.91, A.356, N.357, V.358 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain C: Y.300, D.391, Y.392, D.393 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain C: R.464, N.466 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain C: D.391, F.394, Y.395, G.457, N.460 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain C: G.451, D.452, T.455 Ligand excluded by PLIP EDO.25: 8 residues within 4Å: Chain C: R.70, Y.71, I.89, N.90, S.91, A.356, N.357, V.358 Ligand excluded by PLIP EDO.26: 7 residues within 4Å: Chain C: N.105, R.107, R.230, H.231, G.234, S.235, A.236 Ligand excluded by PLIP EDO.29: 4 residues within 4Å: Chain D: Y.300, D.391, Y.392, D.393 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain D: D.391, F.394, Y.395, G.457, N.460 Ligand excluded by PLIP EDO.31: 7 residues within 4Å: Chain D: N.105, R.107, R.230, H.231, G.234, S.235, A.236 Ligand excluded by PLIP EDO.32: 7 residues within 4Å: Chain D: R.70, I.89, N.90, S.91, A.356, N.357, V.358 Ligand excluded by PLIP EDO.33: 3 residues within 4Å: Chain D: G.451, D.452, T.455 Ligand excluded by PLIP EDO.34: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain E: Y.300, D.391, Y.392, D.393 Ligand excluded by PLIP EDO.38: 3 residues within 4Å: Chain E: G.451, D.452, T.455 Ligand excluded by PLIP EDO.39: 5 residues within 4Å: Chain E: V.179, Q.197, F.198, D.199, T.205 Ligand excluded by PLIP EDO.40: 5 residues within 4Å: Chain E: D.391, F.394, Y.395, G.457, N.460 Ligand excluded by PLIP EDO.41: 7 residues within 4Å: Chain E: N.105, R.107, R.230, H.231, G.234, S.235, A.236 Ligand excluded by PLIP EDO.42: 6 residues within 4Å: Chain A: R.411, N.415 Chain E: R.107, L.111, N.218, L.220 Ligand excluded by PLIP EDO.43: 3 residues within 4Å: Chain E: D.373, L.374, N.375 Ligand excluded by PLIP

5 x ALA: ALANINE(Non-covalent)

ALA.10: 7 residues within 4Å: Chain A: C.9, D.31, T.99, T.101, E.121, N.191 Ligands: PRO.11 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:C.9, A:T.101, A:T.101, A:E.121, A:N.191 ALA.19: 7 residues within 4Å: Chain B: C.9, D.31, T.99, T.101, E.121, N.191 Ligands: PRO.20 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:C.9, B:T.101, B:E.121, B:N.191 ALA.27: 6 residues within 4Å: Chain C: C.9, T.99, T.101, E.121, N.191 Ligands: PRO.28 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:C.9, C:T.101, C:E.121, C:N.191 ALA.35: 6 residues within 4Å: Chain D: C.9, T.99, T.101, E.121, N.191 Ligands: PRO.36 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:C.9, D:T.101, D:T.101, D:E.121, D:N.191 ALA.45: 6 residues within 4Å: Chain E: C.9, T.99, T.101, E.121, N.191 Ligands: PRO.46 6 PLIP interactions: 5 interactions with chain E, 1 Ligand-Ligand interactions Hydrogen bonds: E:C.9, E:T.101, E:T.101, E:E.121, E:N.191, P.46

5 x PRO: PROLINE(Non-covalent)

PRO.11: 8 residues within 4Å: Chain A: C.9, D.31, T.101, N.191, Y.243, R.312, R.318 Ligands: ALA.10 5 PLIP interactions: 5 interactions with chain A, Hydrogen bonds: A:C.9, A:T.101, A:N.191 Salt bridges: A:R.312, A:R.318 PRO.20: 8 residues within 4Å: Chain B: C.9, D.31, T.101, N.191, Y.243, R.312, R.318 Ligands: ALA.19 4 PLIP interactions: 4 interactions with chain B, Hydrogen bonds: B:T.101, B:N.191 Salt bridges: B:R.312, B:R.318 PRO.28: 8 residues within 4Å: Chain C: C.9, D.31, T.101, N.191, Y.243, R.312, R.318 Ligands: ALA.27 5 PLIP interactions: 5 interactions with chain C, Hydrogen bonds: C:C.9, C:T.101, C:N.191 Salt bridges: C:R.312, C:R.318 PRO.36: 8 residues within 4Å: Chain D: C.9, D.31, T.101, N.191, Y.243, R.312, R.318 Ligands: ALA.35 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Ligand interactions Hydrogen bonds: D:C.9, D:T.101, P.36 Salt bridges: D:R.312, D:R.318 PRO.46: 7 residues within 4Å: Chain E: C.9, T.101, N.191, Y.243, R.312, R.318 Ligands: ALA.45 8 PLIP interactions: 2 Ligand-Ligand interactions, 6 interactions with chain E Hydrogen bonds: A.45, P.46, E:C.9, E:T.101 Hydrophobic interactions: E:T.101 Water bridges: E:Y.243 Salt bridges: E:R.312, E:R.318

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

ACT.44: 4 residues within 4Å: Chain E: L.374, N.375, F.443, N.447 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:F.443 Hydrogen bonds: E:N.447

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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