SMTL ID : 5m4l.1

Crystal Structure of Wild-Type Human Prolidase with Mg ions and LeuPro ligand

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 9 residues within 4Å: Chain A: D.282, H.365, T.405, E.407, E.447 Ligands: MG.2, OH.3, LEU.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.407, OH.3, LEU.4 MG.2: 8 residues within 4Å: Chain A: Y.236, D.271, D.282, T.284, E.447 Ligands: MG.1, OH.3, LEU.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 MG.10: 9 residues within 4Å: Chain B: D.282, H.365, T.405, E.407, E.447 Ligands: MG.11, OH.12, LEU.13, PRO.14 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Ligand interactions Metal complexes: B:D.282, B:H.365, B:E.407, OH.12, LEU.13 MG.11: 8 residues within 4Å: Chain B: Y.236, D.271, D.282, T.284, E.447 Ligands: MG.10, OH.12, LEU.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: MG.1, MG.2, LEU.4, PRO.5 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:E.407, L.4 OH.12: 8 residues within 4Å: Chain B: D.271, D.282, E.407, E.447 Ligands: MG.10, MG.11, LEU.13, PRO.14 2 PLIP interactions: 2 Ligand-Ligand interactions Hydrogen bonds: L.13, L.13

2 x LEU: LEUCINE(Non-covalent)

LEU.4: 12 residues within 4Å: Chain A: Y.236, I.239, H.250, D.271, D.282, H.365, V.371, H.372 Ligands: MG.1, MG.2, OH.3, PRO.5 4 PLIP interactions: 4 interactions with chain A, Hydrophobic interactions: A:Y.236, A:I.239, A:V.371 Hydrogen bonds: A:Y.236 LEU.13: 13 residues within 4Å: Chain B: Y.236, I.239, H.250, D.271, D.282, H.365, V.371, H.372, E.407 Ligands: MG.10, MG.11, OH.12, PRO.14 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.236, B:I.239, B:V.371 Hydrogen bonds: B:Y.236

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: MG.1, OH.3, LEU.4 5 PLIP interactions: 1 Ligand-Ligand interactions, 4 interactions with chain A Hydrogen bonds: P.5 Hydrophobic interactions: A:H.361 Salt bridges: A:H.250, A:H.372, A:R.393 PRO.14: 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: MG.10, OH.12, LEU.13 5 PLIP interactions: 5 interactions with chain B, Hydrophobic interactions: B:H.361 Water bridges: B:E.407 Salt bridges: B:H.250, B:H.372, B:R.393

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: S.3, F.4, W.5, L.6, K.115 Chain B: P.257, D.259 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.3, A:W.5 Water bridges: A:T.73 GOL.7: 5 residues within 4Å: Chain A: T.147, Y.377, V.381, 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.8: 3 residues within 4Å: Chain A: S.129, T.132, S.133 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.129 GOL.9: 5 residues within 4Å: Chain A: F.158, D.159, G.160, I.161, S.162 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.160, A:I.161, A:S.162, A:S.162 GOL.15: 5 residues within 4Å: Chain B: A.337, H.338, G.340, L.342, S.343 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.342 Water bridges: B:E.334, B:H.338 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 GOL.17: 6 residues within 4Å: Chain A: D.259 Chain B: S.3, F.4, W.5, L.6, K.115 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.259, B:S.3, B:W.5 Water bridges: B:T.73

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

NA.18: 2 residues within 4Å: Chain B: K.206, M.474 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.474

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

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