SMTL ID : 6nff.1

Structure of X-prolyl dipeptidyl aminopeptidase from Lactobacillus helveticus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.214, D.216, D.218, K.220, D.222 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.216, A:D.218, A:K.220, A:D.222, H2O.10 CA.23: 5 residues within 4Å: Chain B: D.214, D.216, D.218, K.220, D.222 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.216, B:D.218, B:K.220, B:D.222, H2O.31

8 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 4 residues within 4Å: Chain A: H.419, K.509, K.513, R.668 9 PLIP interactions: 9 interactions with chain A Water bridges: A:H.419, A:K.509, A:K.513, A:R.668, A:L.764 Salt bridges: A:H.419, A:K.509, A:K.513, A:R.668 PO4.3: 4 residues within 4Å: Chain A: N.483, R.485, H.486, K.513 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.483 Salt bridges: A:R.485, A:H.486, A:K.513 PO4.4: 2 residues within 4Å: Chain A: H.261, N.262 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.262 Water bridges: A:R.259, A:H.261 Salt bridges: A:H.261 PO4.5: 3 residues within 4Å: Chain A: H.706 Chain B: H.706 Ligands: PO4.27 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Salt bridges: B:H.706, A:H.706 Water bridges: A:T.719, A:T.719 PO4.24: 4 residues within 4Å: Chain B: H.419, K.509, K.513, R.668 10 PLIP interactions: 10 interactions with chain B Water bridges: B:D.414, B:D.414, B:H.419, B:K.513, B:R.668, B:L.764 Salt bridges: B:H.419, B:K.509, B:K.513, B:R.668 PO4.25: 4 residues within 4Å: Chain B: N.483, R.485, H.486, K.513 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.483 Salt bridges: B:R.485, B:H.486, B:K.513 PO4.26: 2 residues within 4Å: Chain B: H.261, N.262 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.262 Water bridges: B:R.259, B:H.261 Salt bridges: B:H.261 PO4.27: 3 residues within 4Å: Chain A: H.706 Chain B: H.706 Ligands: PO4.5 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:H.706, A:H.706 Water bridges: A:T.719

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

EDO.6: 9 residues within 4Å: Chain A: P.307, L.308, N.538, N.539, T.546, Q.709, L.711, D.718 Ligands: EDO.10 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: F.83, Q.113, L.114, K.174 Chain B: R.328 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: A.300, V.301, K.303 Chain B: G.173, E.710 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: V.119, H.120, D.124, F.125 Chain B: Y.450 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: G.164, Q.165, Y.311, N.538, T.546, Q.709 Ligands: EDO.6 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: N.44, F.45, P.47, K.61, N.65 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: Y.249, S.383, Y.384, Y.415 Ligands: EDO.22 Ligand excluded by PLIP EDO.13: 2 residues within 4Å: Chain A: N.77, A.92 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: E.69, K.79 Chain B: Q.225, E.298, V.301, R.328 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain A: N.256, E.257, N.260, A.427, C.428, E.431 Ligands: EDO.22 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: H.583, E.584, E.585, K.813 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain A: K.71, K.174, G.175, T.178, Y.713 Chain B: E.299 Ligands: EDO.20 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain A: Y.278, T.336, G.337, A.338, F.478, A.481, G.482 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain A: G.604, S.651, L.652, R.653, F.654 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain A: A.68, K.71, G.175, Y.176 Ligands: EDO.17 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain A: L.267, S.268, S.270, N.471, T.472, N.740, K.791 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain A: Y.415, C.428, E.431, N.505 Ligands: EDO.12, EDO.15 Ligand excluded by PLIP EDO.28: 9 residues within 4Å: Chain B: P.307, L.308, N.538, N.539, T.546, Q.709, L.711, D.718 Ligands: EDO.32 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain A: R.328 Chain B: F.83, Q.113, L.114, K.174 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain A: G.173, E.710 Chain B: A.300, V.301, K.303 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain A: Y.450 Chain B: V.119, H.120, D.124, F.125 Ligand excluded by PLIP EDO.32: 7 residues within 4Å: Chain B: G.164, Q.165, Y.311, N.538, T.546, Q.709 Ligands: EDO.28 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain B: N.44, F.45, P.47, K.61, N.65 Ligand excluded by PLIP EDO.34: 5 residues within 4Å: Chain B: Y.249, S.383, Y.384, Y.415 Ligands: EDO.44 Ligand excluded by PLIP EDO.35: 2 residues within 4Å: Chain B: N.77, A.92 Ligand excluded by PLIP EDO.36: 6 residues within 4Å: Chain A: Q.225, E.298, V.301, R.328 Chain B: E.69, K.79 Ligand excluded by PLIP EDO.37: 7 residues within 4Å: Chain B: N.256, E.257, N.260, A.427, C.428, E.431 Ligands: EDO.44 Ligand excluded by PLIP EDO.38: 4 residues within 4Å: Chain B: H.583, E.584, E.585, K.813 Ligand excluded by PLIP EDO.39: 7 residues within 4Å: Chain A: E.299 Chain B: K.71, K.174, G.175, T.178, Y.713 Ligands: EDO.42 Ligand excluded by PLIP EDO.40: 7 residues within 4Å: Chain B: Y.278, T.336, G.337, A.338, F.478, A.481, G.482 Ligand excluded by PLIP EDO.41: 5 residues within 4Å: Chain B: G.604, S.651, L.652, R.653, F.654 Ligand excluded by PLIP EDO.42: 5 residues within 4Å: Chain B: A.68, K.71, G.175, Y.176 Ligands: EDO.39 Ligand excluded by PLIP EDO.43: 7 residues within 4Å: Chain B: L.267, S.268, S.270, N.471, T.472, N.740, K.791 Ligand excluded by PLIP EDO.44: 6 residues within 4Å: Chain B: Y.415, C.428, E.431, N.505 Ligands: EDO.34, EDO.37 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ojennus, D.D. et al., Structural characterization of a prolyl aminodipeptidase (PepX) from Lactobacillus helveticus. Acta Crystallogr.,Sect.F (2019)

Release Date

2019-10-02

Peptides

Xaa-Pro dipeptidyl-peptidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Xaa-Pro dipeptidyl-peptidase