SMTL ID : 5mc5.1

Crystal Structure of delGlu452 mutant of Human Prolidase with Mn ions and GlyPro ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 8 residues within 4Å: Chain A: D.282, H.365, E.407, E.447 Ligands: MN.2, OH.3, GLY.4, PRO.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: A:D.282, A:H.365, A:E.447, OH.3, GLY.4 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:D.282, OH.3 MN.7: 8 residues within 4Å: Chain B: D.282, H.365, E.407, E.447 Ligands: MN.8, OH.9, GLY.10, PRO.11 5 PLIP interactions: 2 Ligand-Ligand interactions, 3 interactions with chain B Metal complexes: OH.9, GLY.10, B:D.282, B:H.365, B:E.407 MN.8: 8 residues within 4Å: Chain B: Y.236, D.271, D.282, T.284, E.447 Ligands: MN.7, OH.9, GLY.10 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.271, B:D.271, B:D.282, B:D.282, OH.9

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.9: 9 residues within 4Å: Chain B: D.271, D.282, T.284, E.407, E.447 Ligands: MN.7, MN.8, GLY.10, PRO.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.282, B:T.284

2 x GLY: GLYCINE(Non-covalent)

GLY.4: 11 residues within 4Å: Chain A: Y.236, I.239, H.250, D.271, D.282, H.365, H.372 Ligands: MN.1, MN.2, OH.3, PRO.5 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.250 GLY.10: 11 residues within 4Å: Chain B: Y.236, I.239, H.250, D.271, D.282, H.365, H.372 Ligands: MN.7, MN.8, OH.9, PRO.11 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain B Water bridges: G.10 Hydrogen bonds: B:D.271

2 x PRO: PROLINE(Non-covalent)

PRO.5: 12 residues within 4Å: Chain A: L.249, H.250, D.271, H.361, H.372, R.393, E.407, R.445 Chain B: W.102 Ligands: MN.1, OH.3, GLY.4 4 PLIP interactions: 4 interactions with chain A, Hydrophobic interactions: A:H.361 Salt bridges: A:H.250, A:H.372, A:R.393 PRO.11: 12 residues within 4Å: Chain A: W.102 Chain B: L.249, H.250, D.271, H.361, H.372, R.393, E.407, R.445 Ligands: MN.7, OH.9, GLY.10 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:H.361 Salt bridges: B:H.250, B:H.372, B:R.393 Hydrogen bonds: P.11

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: T.147, Y.377, R.383 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.147, A:R.383 Water bridges: A:Y.377, A:R.383 GOL.12: 5 residues within 4Å: Chain B: K.109, E.110, D.120, V.121, Q.122 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.110 Water bridges: B:D.120, B:D.120, B:Q.122, B:Q.122

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