SMTL ID : 6h2q.1

Crystal Structure of Arg184Gln mutant of Human Prolidase with Mn ions and LeuPro ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 8 residues within 4Å: Chain A: D.287, H.370, T.410, E.412, E.452 Ligands: MN.2, LEU.6, PRO.7 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.287, A:H.370, A:E.412, A:E.452, LEU.6 MN.2: 7 residues within 4Å: Chain A: Y.241, D.276, D.287, T.289, E.452 Ligands: MN.1, LEU.6 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.276, A:D.276, A:D.287, A:E.452, LEU.6 MN.8: 8 residues within 4Å: Chain B: D.287, H.370, T.410, E.412, E.452 Ligands: MN.9, LEU.10, PRO.11 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.287, B:H.370, B:E.412, B:E.452, LEU.10 MN.9: 7 residues within 4Å: Chain B: Y.241, D.276, D.287, T.289, E.452 Ligands: MN.8, LEU.10 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.276, B:D.276, B:D.287, B:E.452, LEU.10

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: Y.83, V.129, D.130, I.132, S.162, F.163, D.164 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.164, A:D.164 Water bridges: A:D.130, A:I.132 GOL.4: 9 residues within 4Å: Chain A: Q.49, G.50, G.51, E.52, E.68, R.159, E.160, A.161 Chain B: Y.57 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.160 Water bridges: A:Q.49, A:Q.49, A:G.50, A:S.162 GOL.5: 7 residues within 4Å: Chain A: S.8, F.9, W.10, L.11, K.120 Chain B: P.262, D.264 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.8, A:W.10 Water bridges: A:T.78

2 x LEU: LEUCINE(Non-covalent)

LEU.6: 15 residues within 4Å: Chain A: Y.241, I.244, H.255, D.276, D.287, H.370, V.376, H.377, E.412, E.452 Chain B: T.61, G.62 Ligands: MN.1, MN.2, PRO.7 7 PLIP interactions: 6 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.241, A:V.376 Hydrogen bonds: A:D.287, L.6 Salt bridges: A:H.255, A:H.370, A:H.377 LEU.10: 16 residues within 4Å: Chain A: D.60, T.61, G.62 Chain B: Y.241, I.244, H.255, D.276, D.287, H.370, V.376, H.377, E.412, E.452 Ligands: MN.8, MN.9, PRO.11 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:V.376, B:V.376 Hydrogen bonds: B:D.276, L.10 Salt bridges: B:H.370, B:H.377

2 x PRO: PROLINE(Non-covalent)

PRO.7: 13 residues within 4Å: Chain A: L.254, H.255, H.366, G.367, H.370, H.377, R.398, E.412, Y.416, R.450 Chain B: W.107 Ligands: MN.1, LEU.6 9 PLIP interactions: 5 interactions with chain A, 4 Ligand-Ligand interactions Hydrophobic interactions: A:H.366 Hydrogen bonds: A:H.255, P.7, P.7, P.7, P.7 Salt bridges: A:H.255, A:H.377, A:R.398 PRO.11: 13 residues within 4Å: Chain A: W.107 Chain B: L.254, H.255, H.366, G.367, H.370, H.377, R.398, E.412, Y.416, R.450 Ligands: MN.8, LEU.10 7 PLIP interactions: 2 Ligand-Ligand interactions, 5 interactions with chain B Hydrogen bonds: P.11, P.11, B:H.255 Hydrophobic interactions: B:H.366 Salt bridges: B:H.255, B:H.377, B:R.398

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

2018-08-15

Peptides

Xaa-Pro dipeptidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Xaa-Pro dipeptidase