SMTL ID : 5mbz.1

Crystal Structure of Ser202Phe mutant of Human Prolidase with Mn ions and GlyPro ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 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: 2 Ligand-Ligand interactions, 3 interactions with chain A Metal complexes: OH.3, GLY.4, A:D.282, A:E.407, A:E.447 MN.2: 7 residues within 4Å: Chain A: 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, E.407, E.447 Ligands: MN.11, OH.12, GLY.13, PRO.14 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Ligand interactions Metal complexes: B:D.282, B:E.407, B:E.447, OH.12, GLY.13 MN.11: 7 residues within 4Å: Chain B: 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.282, 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.284 OH.12: 9 residues within 4Å: Chain B: D.271, D.282, E.407, R.445, 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: 10 residues within 4Å: Chain A: I.239, D.271, D.282, H.365, H.372, E.407 Ligands: MN.1, MN.2, OH.3, PRO.5 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain A Water bridges: G.4 Hydrogen bonds: A:D.271 GLY.13: 9 residues within 4Å: Chain B: D.271, D.282, H.365, H.372, E.407 Ligands: MN.10, MN.11, OH.12, PRO.14 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain B Water bridges: G.13 Hydrogen bonds: B:D.271

2 x PRO: PROLINE(Non-covalent)

PRO.5: 11 residues within 4Å: Chain A: L.249, H.250, 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.14: 11 residues within 4Å: Chain B: L.249, H.250, D.271, H.361, H.372, R.393, E.407, R.445 Ligands: MN.10, OH.12, GLY.13 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.14

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: T.147, Y.377, E.382, R.383 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.147, A:E.382, A:R.383, A:R.383 GOL.7: 2 residues within 4Å: Chain A: H.107, K.115 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.115 Water bridges: A:T.73, A:T.73, A:T.73, A:K.115 GOL.15: 5 residues within 4Å: Chain B: R.143, G.144, N.168, T.169, P.173 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.168, B:T.169 GOL.16: 4 residues within 4Å: Chain B: T.147, Y.377, E.382, R.383 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.147, B:E.382, B:R.383, B:R.383, B:R.383

2 x NA: SODIUM ION(Non-functional Binders)

NA.8: 2 residues within 4Å: Chain A: K.206, M.474 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.206 NA.9: 2 residues within 4Å: Chain A: A.427, L.430 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.427

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.17: 4 residues within 4Å: Chain B: R.432, L.435, Q.436, R.439 Ligand excluded by PLIP

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

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