SMTL ID : 6srf.1

Crystal Structure of Human Prolidase G278N variant expressed in the presence of chaperones

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 9 residues within 4Å: Chain A: D.282, H.365, H.372, T.405, E.407, E.447 Ligands: NA.2, GLY.4, PRO.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.282, A:H.365, A:E.407, A:E.447, GLY.4 MN.6: 9 residues within 4Å: Chain B: D.282, H.365, H.372, T.405, E.407, E.447 Ligands: NA.7, GLY.8, PRO.9 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.282, B:H.365, B:E.407, B:E.447, GLY.8

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

NA.2: 9 residues within 4Å: Chain A: D.271, D.282, T.284, E.407, R.445, E.447 Ligands: MN.1, GLY.4, PRO.5 3 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain A Hydrogen bonds: G.4, A:T.284, A:E.447 NA.7: 9 residues within 4Å: Chain B: D.271, D.282, T.284, E.407, R.445, E.447 Ligands: MN.6, GLY.8, PRO.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.284, B:T.284

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: T.147, Y.377, E.382, R.383 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.147, A:R.383, A:R.383 Water bridges: A:R.383

2 x GLY: GLYCINE(Non-covalent)

GLY.4: 13 residues within 4Å: Chain A: Y.236, I.239, H.250, D.271, D.282, H.365, V.371, H.372, E.407, R.445 Ligands: MN.1, NA.2, PRO.5 3 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain A Hydrogen bonds: G.4, A:D.282, A:H.372 GLY.8: 13 residues within 4Å: Chain B: Y.236, I.239, H.250, D.271, D.282, H.365, V.371, H.372, E.407, R.445 Ligands: MN.6, NA.7, PRO.9 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:Y.236, B:H.372, G.8

2 x PRO: PROLINE(Non-covalent)

PRO.5: 15 residues within 4Å: Chain A: I.239, L.249, H.250, D.271, H.361, G.362, H.365, H.372, R.393, E.407, R.445 Chain B: W.102 Ligands: MN.1, NA.2, GLY.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:H.361 Hydrogen bonds: A:H.250 Salt bridges: A:H.250, A:H.372, A:R.393 PRO.9: 15 residues within 4Å: Chain A: W.102 Chain B: I.239, L.249, H.250, D.271, H.361, G.362, H.365, H.372, R.393, E.407, R.445 Ligands: MN.6, NA.7, GLY.8 7 PLIP interactions: 6 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:H.361 Hydrogen bonds: B:H.250, P.9 Water bridges: B:G.362 Salt bridges: B:H.250, B:H.372, B:R.393

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