SMTL ID : 5m4q.1

Crystal Structure of Wild-Type Human Prolidase with Mn ions and Pro ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 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: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:D.282, A:H.365, A:E.407, H2O.1, OH.3 MN.2: 7 residues within 4Å: Chain A: Y.236, D.271, D.282, T.284, 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.11 MN.9: 7 residues within 4Å: Chain B: D.282, H.365, T.405, E.407, E.447 Ligands: MN.10, OH.11 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.282, B:H.365, B:E.407, B:E.447, H2O.18 MN.10: 7 residues within 4Å: Chain B: Y.236, D.271, D.282, T.284, E.447 Ligands: MN.9, OH.11 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.11, H2O.27

2 x OH: HYDROXIDE ION(Non-covalent)

OH.3: 7 residues within 4Å: Chain A: D.271, D.282, E.407, E.447 Ligands: MN.1, MN.2, PRO.4 No protein-ligand interaction detected (PLIP) OH.11: 7 residues within 4Å: Chain B: D.271, D.282, E.407, E.447 Ligands: MN.9, MN.10, PRO.12 No protein-ligand interaction detected (PLIP)

2 x PRO: PROLINE(Non-covalent)

PRO.4: 9 residues within 4Å: Chain A: H.250, H.361, H.365, H.372, R.393, E.407, R.445 Chain B: W.102 Ligands: OH.3 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:H.361 Hydrogen bonds: A:H.250, P.4 Salt bridges: A:H.250, A:H.372, A:R.393 PRO.12: 9 residues within 4Å: Chain A: W.102 Chain B: H.250, D.271, H.361, H.372, R.393, E.407, R.445 Ligands: OH.11 8 PLIP interactions: 5 interactions with chain B, 3 Ligand-Ligand interactions Hydrophobic interactions: B:H.361 Hydrogen bonds: B:H.250, P.12, P.12, P.12 Salt bridges: B:H.250, B:H.372, B:R.393

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: F.4, W.5, L.6, K.115 Chain B: P.257, D.259 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.259, B:D.259, A:S.3, A:W.5 Water bridges: A:K.115 GOL.6: 7 residues within 4Å: Chain A: H.325, R.326, D.329, H.353, E.386, P.387, L.389 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.329, A:D.329, A:H.353 GOL.7: 5 residues within 4Å: Chain A: T.147, Y.377, V.381, E.382, R.383 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.147, A:E.382, A:R.383, A:R.383, A:R.383 GOL.8: 5 residues within 4Å: Chain A: A.337, H.338, G.340, L.342, S.343 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.342 GOL.13: 6 residues within 4Å: Chain A: D.259 Chain B: S.3, F.4, W.5, L.6, K.115 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:W.5, B:W.5, B:K.115, B:K.115 Water bridges: B:T.73, B:T.73, B:T.73 GOL.14: 4 residues within 4Å: Chain B: F.158, G.160, I.161, S.162 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.160, B:I.161, B:S.162, B:S.162 Water bridges: B:S.157, B:S.157 GOL.15: 7 residues within 4Å: Chain A: E.222, H.223, Y.226, R.232 Chain B: S.219, E.222, H.223 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

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