SMTL ID : 5mby.1

Crystal Structure of Arg184Gln mutant of Human Prolidase with Mn ions and GlyPro ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 7 residues within 4Å: Chain A: D.282, H.365, T.405, E.407, E.447 Ligands: MN.2, OH.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.282, A:H.365, A:E.407, A:E.447, OH.3 MN.2: 8 residues within 4Å: Chain A: Y.236, D.271, D.282, T.284, E.447 Ligands: MN.1, OH.3, GLY.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.271, A:D.271, A:D.282, A:E.447, OH.3 MN.10: 8 residues within 4Å: Chain B: D.282, H.365, T.405, E.407, E.447 Ligands: MN.11, OH.12, GLY.13 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.282, B:H.365, B:E.407, B:E.447, OH.12 MN.11: 8 residues within 4Å: Chain B: Y.236, D.271, D.282, T.284, E.447 Ligands: MN.10, OH.12, GLY.13 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.271, B:D.271, B:D.282, B:E.447, OH.12

2 x OH: HYDROXIDE ION(Non-covalent)

OH.3: 8 residues within 4Å: Chain A: D.271, D.282, E.407, E.447 Ligands: MN.1, MN.2, GLY.4, PRO.5 No protein-ligand interaction detected (PLIP) OH.12: 8 residues within 4Å: Chain B: D.271, D.282, E.407, E.447 Ligands: MN.10, MN.11, GLY.13, PRO.14 No protein-ligand interaction detected (PLIP)

2 x GLY: GLYCINE(Non-covalent)

GLY.4: 9 residues within 4Å: Chain A: Y.236, I.239, H.250, D.271, D.282, H.372 Ligands: MN.2, OH.3, PRO.5 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:Y.236, P.5, P.5 Water bridges: A:T.237 Salt bridges: A:H.250, A:H.372 GLY.13: 10 residues within 4Å: Chain B: Y.236, I.239, H.250, D.271, D.282, H.372 Ligands: MN.10, MN.11, OH.12, PRO.14 4 PLIP interactions: 1 Ligand-Ligand interactions, 3 interactions with chain B Hydrogen bonds: P.14, B:Y.236 Salt bridges: B:H.250, B:H.372

2 x PRO: PROLINE(Non-covalent)

PRO.5: 9 residues within 4Å: Chain A: H.250, H.361, H.372, R.393, E.407, R.445 Chain B: W.102 Ligands: OH.3, GLY.4 8 PLIP interactions: 3 Ligand-Ligand interactions, 5 interactions with chain A Hydrogen bonds: G.4, P.5, P.5, A:H.250 Hydrophobic interactions: A:H.361 Salt bridges: A:H.250, A:H.372, A:R.393 PRO.14: 9 residues within 4Å: Chain A: W.102 Chain B: H.250, H.361, H.372, R.393, E.407, R.445 Ligands: OH.12, GLY.13 6 PLIP interactions: 1 Ligand-Ligand interactions, 5 interactions with chain B Hydrogen bonds: P.14, B:H.250 Hydrophobic interactions: B:H.361 Salt bridges: B:H.250, B:H.372, B:R.393

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: Y.78, V.124, D.125, I.127, F.158, D.159 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.78, A:Y.78, A:V.124, A:D.159 GOL.7: 8 residues within 4Å: Chain A: Q.44, G.45, G.46, E.63, R.154, E.155, A.156 Chain B: Y.52 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.44, A:Q.44 GOL.8: 6 residues within 4Å: Chain A: S.3, F.4, W.5, L.6, K.115 Chain B: D.259 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.5, A:W.5 Water bridges: A:T.73, A:K.115, A:Y.116 GOL.9: 5 residues within 4Å: Chain A: T.147, Y.377, V.381, E.382, R.383 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.147, A:V.381, A:R.383 GOL.15: 5 residues within 4Å: Chain A: Y.52 Chain B: Q.44, R.154, E.155, A.156 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.154 Water bridges: B:Q.44, B:Q.44 GOL.16: 5 residues within 4Å: Chain B: T.147, Y.377, V.381, E.382, R.383 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.147, B:E.382, B:R.383, B:R.383

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wilk, P. et al., Structural basis for prolidase deficiency disease mechanisms. FEBS J. (2018)

Release Date

2017-12-20

Peptides

Xaa-Pro dipeptidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Xaa-Pro dipeptidase