SMTL ID : 5mc3.1

Crystal Structure of Glu412Lys mutant of Human Prolidase with Mn ions and GlyPro ligand

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 8 residues within 4Å: Chain A: Y.236, D.271, D.282, T.284, K.407, E.447 Ligands: OH.2, GLY.3 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.2 MN.10: 8 residues within 4Å: Chain B: Y.236, D.271, D.282, T.284, K.407, E.447 Ligands: OH.11, GLY.12 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.11

2 x OH: HYDROXIDE ION(Non-covalent)

OH.2: 9 residues within 4Å: Chain A: D.271, D.282, T.284, K.407, R.445, E.447 Ligands: MN.1, GLY.3, PRO.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.284, A:K.407, A:R.445 OH.11: 9 residues within 4Å: Chain B: D.271, D.282, T.284, K.407, R.445, E.447 Ligands: MN.10, GLY.12, PRO.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.407, B:K.407

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, K.407 Ligands: MN.1, OH.2, PRO.4 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:D.271 Water bridges: G.3 GLY.12: 11 residues within 4Å: Chain B: Y.236, I.239, H.250, D.271, D.282, H.365, H.372, K.407 Ligands: MN.10, OH.11, PRO.13 3 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain B Water bridges: G.12, B:H.372 Hydrogen bonds: B:K.407

2 x PRO: PROLINE(Non-covalent)

PRO.4: 10 residues within 4Å: Chain A: L.249, H.250, H.361, H.372, R.393, K.407, R.445 Chain B: W.102 Ligands: OH.2, GLY.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:H.361, A:K.407 Salt bridges: A:H.250, A:H.372, A:R.393, A:K.407 PRO.13: 10 residues within 4Å: Chain A: W.102 Chain B: L.249, H.250, H.361, H.372, R.393, K.407, R.445 Ligands: OH.11, GLY.12 7 PLIP interactions: 6 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:H.361 Hydrogen bonds: B:K.407, P.13 Salt bridges: B:H.250, B:H.372, B:R.393, B:K.407

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

NA.5: 3 residues within 4Å: Chain A: G.230, Y.276, Y.277 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.230, A:Y.277 Water bridges: A:R.232, A:C.278 NA.14: 3 residues within 4Å: Chain B: K.206, M.474 Ligands: GOL.16 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.206

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: S.3, F.4, W.5, L.6, K.115 Chain B: D.259 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.259, A:W.5, A:W.5 GOL.7: 6 residues within 4Å: Chain A: G.104, K.105 Chain B: N.245, V.248, A.256, D.259 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.259, A:K.105 Water bridges: B:N.245 GOL.8: 3 residues within 4Å: Chain A: D.385, P.387, R.390 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.390, A:R.390 GOL.9: 4 residues within 4Å: Chain A: T.147, Y.377, 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.15: 5 residues within 4Å: Chain B: R.30, V.35, Q.36, A.37, D.84 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.37 GOL.16: 8 residues within 4Å: Chain B: V.208, K.209, V.210, A.289, N.290, G.291, M.474 Ligands: NA.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.210, B:M.474 GOL.17: 4 residues within 4Å: Chain B: G.344, S.345, V.346, D.347 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.344, B:S.345, B:V.346, B:D.347, B:D.347 Water bridges: B:S.345 GOL.18: 5 residues within 4Å: Chain B: G.265, R.437, R.439, G.440, F.441 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.265 Water bridges: B:G.265, B:D.266, B:M.267, B:Q.297 GOL.19: 8 residues within 4Å: Chain B: K.182, T.183, D.184, L.187, G.401, V.451, V.452, T.453 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.184, B:G.401 GOL.20: 5 residues within 4Å: Chain B: T.147, Y.377, V.381, E.382, R.383 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.147, B:E.382, B:R.383, B:R.383

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