SMTL ID : 5m4g.1

Crystal Structure of Wild-Type Human Prolidase with Mn ions

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

homo-dimer

Ligands

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 6 residues within 4Å: Chain A: D.282, H.365, E.407, E.447 Ligands: MN.2, OH.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.282, A:H.365, A:E.407, A:E.447, H2O.3 MN.2: 8 residues within 4Å: Chain A: Y.236, D.271, D.282, T.284, E.407, E.447 Ligands: MN.1, OH.3 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:D.271, A:D.282, A:E.447, OH.3, H2O.8 MN.7: 6 residues within 4Å: Chain B: D.282, H.365, E.407, E.447 Ligands: MN.8, OH.9 5 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:D.282, B:E.407, B:E.447, OH.9, H2O.24 MN.8: 7 residues within 4Å: Chain B: Y.236, D.271, D.282, T.284, E.447 Ligands: MN.7, OH.9 5 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:D.271, B:D.282, B:E.447, OH.9, H2O.31

2 x OH: HYDROXIDE ION(Non-covalent)

OH.3: 6 residues within 4Å: Chain A: D.271, D.282, E.407, E.447 Ligands: MN.1, MN.2 No protein-ligand interaction detected (PLIP) OH.9: 6 residues within 4Å: Chain B: D.271, D.282, E.407, E.447 Ligands: MN.7, MN.8 No protein-ligand interaction detected (PLIP)

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: S.157, F.158, D.159, G.160, I.161, S.162 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.157, A:D.159, A:D.159, A:G.160, A:S.162, A:S.162 GOL.5: 7 residues within 4Å: Chain A: S.3, F.4, W.5, L.6, K.115 Chain B: P.257, D.259 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.3, A:W.5, B:D.259, B:D.259 Water bridges: A:K.115 GOL.6: 6 residues within 4Å: Chain A: W.320, P.322, D.323, R.326, E.386, L.389 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.322, A:R.326, A:E.386 GOL.10: 6 residues within 4Å: Chain A: D.259 Chain B: S.3, F.4, W.5, L.6, K.115 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:W.5, B:W.5, A:D.259 Water bridges: B:T.73, B:K.115, B:Y.116 GOL.11: 5 residues within 4Å: Chain B: F.158, D.159, G.160, I.161, S.162 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.159, B:G.160, B:S.162, B:S.162 Water bridges: B:S.157, B:S.157 GOL.12: 6 residues within 4Å: Chain B: E.222, Y.226, R.232, H.233, S.234 Ligands: GOL.13 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.222, B:S.234, B:S.234 Water bridges: B:E.222, B:R.232 GOL.13: 8 residues within 4Å: Chain A: E.222, H.223, Y.226, R.232 Chain B: S.219, E.222, H.223 Ligands: GOL.12 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.219, B:E.222, A:H.223, A:R.232

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wilk, P. et al., Substrate specificity and reaction mechanism of human prolidase. FEBS J. (2017)

Release Date

2017-07-12

Peptides

Xaa-Pro dipeptidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Xaa-Pro dipeptidase