SMTL ID : 5mc0.1

Crystal Structure of delTyr231 mutant of Human Prolidase with Mn ions and GlyPro ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 8 residues within 4Å: Chain A: D.281, H.364, E.406, E.446 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.281, A:H.364, A:E.446 MN.2: 9 residues within 4Å: Chain A: Y.235, D.270, D.281, T.283, E.406, E.446 Ligands: MN.1, OH.3, GLY.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.270, A:D.270, A:D.281, A:E.446, OH.3 MN.12: 8 residues within 4Å: Chain B: D.281, H.364, E.406, E.446 Ligands: MN.13, OH.14, GLY.15, PRO.16 5 PLIP interactions: 2 Ligand-Ligand interactions, 3 interactions with chain B Metal complexes: OH.14, GLY.15, B:D.281, B:E.406, B:E.446 MN.13: 8 residues within 4Å: Chain B: Y.235, D.270, D.281, T.283, E.446 Ligands: MN.12, OH.14, GLY.15 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.270, B:D.270, B:D.281, B:E.446, OH.14

2 x OH: HYDROXIDE ION(Non-covalent)

OH.3: 9 residues within 4Å: Chain A: D.270, D.281, E.406, R.444, E.446 Ligands: MN.1, MN.2, GLY.4, PRO.5 No protein-ligand interaction detected (PLIP) OH.14: 9 residues within 4Å: Chain B: D.270, D.281, E.406, R.444, E.446 Ligands: MN.12, MN.13, GLY.15, PRO.16 No protein-ligand interaction detected (PLIP)

2 x GLY: GLYCINE(Non-covalent)

GLY.4: 12 residues within 4Å: Chain A: Y.235, I.238, H.249, D.270, D.281, H.364, H.371, E.406 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.270 GLY.15: 12 residues within 4Å: Chain B: Y.235, I.238, H.249, D.270, D.281, H.364, H.371, E.406 Ligands: MN.12, MN.13, OH.14, PRO.16 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain B Water bridges: G.15 Hydrogen bonds: B:D.270

2 x PRO: PROLINE(Non-covalent)

PRO.5: 12 residues within 4Å: Chain A: L.248, H.249, D.270, H.360, H.371, R.392, E.406, R.444 Chain B: W.102 Ligands: MN.1, OH.3, GLY.4 4 PLIP interactions: 4 interactions with chain A, Hydrophobic interactions: A:H.360 Salt bridges: A:H.249, A:H.371, A:R.392 PRO.16: 12 residues within 4Å: Chain A: W.102 Chain B: L.248, H.249, D.270, H.360, H.371, R.392, E.406, R.444 Ligands: MN.12, OH.14, GLY.15 8 PLIP interactions: 3 Ligand-Ligand interactions, 5 interactions with chain B Hydrogen bonds: P.16, P.16, P.16, B:H.249 Hydrophobic interactions: B:H.360 Salt bridges: B:H.249, B:H.371, B:R.392

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: F.4, W.5, L.6, K.115 Chain B: P.256, D.258 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:W.5, A:W.5, B:D.258, B:D.258 Water bridges: A:T.73, A:K.115 GOL.7: 4 residues within 4Å: Chain A: T.147, Y.376, E.381, R.382 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.147, A:E.381, A:R.382, A:R.382, A:R.382 GOL.8: 5 residues within 4Å: Chain A: W.319, G.379, V.380, E.381, A.394 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.381 Water bridges: A:H.396 GOL.9: 4 residues within 4Å: Chain A: R.24, R.28, E.177, F.181 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.24, A:R.28, A:E.177 Water bridges: A:R.24, A:F.181 GOL.10: 4 residues within 4Å: Chain A: T.132, P.136, K.163, F.164 3 PLIP interactions: 3 interactions with chain A Water bridges: A:P.136, A:S.137, A:K.163 GOL.18: 6 residues within 4Å: Chain A: D.258 Chain B: S.3, F.4, W.5, L.6, K.115 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.3, B:W.5 GOL.19: 5 residues within 4Å: Chain B: E.9, T.10, L.11, Y.192, K.195 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.9 Water bridges: B:T.10, B:T.10, B:K.195 GOL.20: 3 residues within 4Å: Chain B: S.129, T.132, S.133 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.129 GOL.21: 4 residues within 4Å: Chain B: T.147, Y.376, E.381, R.382 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.147, B:E.381, B:E.381, B:R.382, B:R.382 GOL.22: 6 residues within 4Å: Chain B: S.157, F.158, D.159, G.160, I.161, S.162 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.159, B:G.160, B:I.161, B:S.162, B:S.162 Water bridges: B:S.157, B:S.157, B:F.158 GOL.23: 6 residues within 4Å: Chain B: Y.78, V.124, D.125, I.127, F.158, D.159 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.78, B:Y.78, B:V.124, B:D.159, B:D.159 GOL.24: 3 residues within 4Å: Chain B: T.132, K.163, F.164 No protein-ligand interaction detected (PLIP) GOL.25: 4 residues within 4Å: Chain A: H.223 Chain B: L.220, H.223, R.227 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.227

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

NA.11: 2 residues within 4Å: Chain A: G.312, M.314 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.312 NA.26: 4 residues within 4Å: Chain B: M.205, K.206, V.208, M.473 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.205

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

CL.17: 4 residues within 4Å: Chain B: R.431, L.434, Q.435, R.438 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