SMTL ID : 6srg.1

Crystal Structure of Human Prolidase G448R variant expressed in the presence of chaperones

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.56 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 10 residues within 4Å: Chain A: D.287, H.370, H.377, T.410, E.412, E.452 Ligands: MN.2, OH.3, GLY.4, PRO.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: A:D.287, A:H.370, A:E.412, OH.3, GLY.4 MN.2: 9 residues within 4Å: Chain A: Y.241, D.276, D.287, T.289, R.450, E.452 Ligands: MN.1, OH.3, GLY.4 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, OH.3 MN.6: 10 residues within 4Å: Chain B: D.287, H.370, H.377, T.410, E.412, E.452 Ligands: MN.7, OH.8, GLY.9, PRO.10 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Ligand interactions Metal complexes: B:D.287, B:H.370, B:E.412, OH.8, GLY.9 MN.7: 8 residues within 4Å: Chain B: Y.241, D.276, D.287, T.289, E.452 Ligands: MN.6, OH.8, GLY.9 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, OH.8

2 x OH: HYDROXIDE ION(Non-covalent)

OH.3: 10 residues within 4Å: Chain A: D.276, D.287, T.289, E.412, R.450, E.452 Ligands: MN.1, MN.2, GLY.4, PRO.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:D.276, A:R.450, G.4 OH.8: 10 residues within 4Å: Chain B: D.276, D.287, T.289, E.412, R.450, E.452 Ligands: MN.6, MN.7, GLY.9, PRO.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.276

2 x GLY: GLYCINE(Non-covalent)

GLY.4: 13 residues within 4Å: Chain A: Y.241, I.244, D.276, D.287, H.370, V.376, H.377, E.412, R.450 Ligands: MN.1, MN.2, OH.3, PRO.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:D.276, A:H.377, G.4 GLY.9: 13 residues within 4Å: Chain B: Y.241, I.244, D.276, D.287, H.370, V.376, H.377, E.412, R.450 Ligands: MN.6, MN.7, OH.8, PRO.10 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:D.276, B:H.377, G.9

2 x PRO: PROLINE(Non-covalent)

PRO.5: 11 residues within 4Å: Chain A: I.244, D.276, H.366, H.370, H.377, R.398, E.412, R.450 Ligands: MN.1, OH.3, GLY.4 5 PLIP interactions: 5 interactions with chain A, Hydrophobic interactions: A:H.366 Water bridges: A:G.367, A:S.396 Salt bridges: A:H.377, A:R.398 PRO.10: 12 residues within 4Å: Chain B: I.244, D.276, H.366, G.367, H.370, H.377, R.398, E.412, R.450 Ligands: MN.6, OH.8, GLY.9 5 PLIP interactions: 1 Ligand-Ligand interactions, 4 interactions with chain B Hydrogen bonds: P.10 Hydrophobic interactions: B:H.366 Salt bridges: B:H.370, B:H.377, B:R.398

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 5 residues within 4Å: Chain B: T.152, Y.382, V.386, E.387, R.388 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.152, B:V.386, B:R.388, B:R.388, B:R.388

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wator, E. et al., Co-expression with chaperones can affect protein 3D structure as exemplified by loss-of-function variants of human prolidase. Febs Lett. (2020)

Release Date

2020-07-15

Peptides

Xaa-Pro dipeptidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Xaa-Pro dipeptidase