SMTL ID : 5m4j.1

Crystal Structure of Wild-Type Human Prolidase with GlyPro ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 7 residues within 4Å: Chain A: D.282, H.365, E.407, E.447 Ligands: NA.2, GLY.3, PRO.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.282 NA.2: 8 residues within 4Å: Chain A: D.271, D.282, E.407, R.445, E.447 Ligands: NA.1, GLY.3, PRO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.284, A:E.407 NA.6: 7 residues within 4Å: Chain B: D.282, H.365, E.407, E.447 Ligands: NA.7, GLY.8, PRO.9 1 PLIP interactions: 1 Ligand-Ligand interactions Hydrogen bonds: G.8 NA.7: 9 residues within 4Å: Chain B: D.271, D.282, T.284, E.407, R.445, E.447 Ligands: NA.6, GLY.8, PRO.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.284, B:T.284

2 x GLY: GLYCINE(Non-covalent)

GLY.3: 11 residues within 4Å: Chain A: Y.236, I.239, H.250, D.271, D.282, H.365, H.372, E.407 Ligands: NA.1, NA.2, PRO.4 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain A Water bridges: G.3 Hydrogen bonds: A:D.271 GLY.8: 10 residues within 4Å: Chain B: Y.236, I.239, H.250, D.271, D.282, H.365, H.372 Ligands: NA.6, NA.7, PRO.9 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain B Water bridges: G.8, B:H.372

2 x PRO: PROLINE(Non-covalent)

PRO.4: 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: NA.1, NA.2, GLY.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:H.361 Salt bridges: A:H.250, A:H.372, A:R.393 Hydrogen bonds: P.4 PRO.9: 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: NA.6, NA.7, GLY.8 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

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: S.3, F.4, W.5, L.6, K.115 Chain B: D.259 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.3, A:W.5 Water bridges: A:T.73 GOL.10: 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.11: 6 residues within 4Å: Chain A: Y.236, H.250, H.372 Chain B: D.55, T.56, G.57 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.55, B:G.57, B:G.57, A:H.372 Water bridges: A:R.393 GOL.12: 6 residues within 4Å: Chain A: D.259 Chain B: S.3, F.4, W.5, L.6, K.115 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:W.5, B:W.5, A:D.259, A:D.259 Water bridges: B:T.73 GOL.13: 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

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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