SMTL ID : 5mc2.1

Crystal Structure of Gly278Asp mutant of Human Prolidase with Mn ions and GlyPro ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 7 residues within 4Å: Chain A: D.283, H.366, E.408, E.448 Ligands: NA.2, GLY.3, PRO.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.283, A:H.366, A:E.408, A:E.448, GLY.3 MN.8: 7 residues within 4Å: Chain B: D.283, H.366, E.408, E.448 Ligands: NA.9, GLY.10, PRO.11 5 PLIP interactions: 1 Ligand-Ligand interactions, 4 interactions with chain B Metal complexes: GLY.10, B:D.283, B:H.366, B:E.408, B:E.448

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

NA.2: 8 residues within 4Å: Chain A: D.272, D.283, T.285, E.408, E.448 Ligands: MN.1, GLY.3, PRO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.285, A:E.408 NA.9: 8 residues within 4Å: Chain B: D.272, D.283, T.285, E.408, E.448 Ligands: MN.8, GLY.10, PRO.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.285, B:E.448

2 x GLY: GLYCINE(Non-covalent)

GLY.3: 10 residues within 4Å: Chain A: I.240, H.251, D.272, D.283, H.366, H.373, E.408 Ligands: MN.1, NA.2, PRO.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.272 Water bridges: A:D.274, A:D.274, A:D.274 GLY.10: 9 residues within 4Å: Chain B: I.240, D.272, D.283, H.366, H.373, E.408 Ligands: MN.8, NA.9, PRO.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.272 Water bridges: B:D.274, B:D.274, B:D.274

2 x PRO: PROLINE(Non-covalent)

PRO.4: 10 residues within 4Å: Chain A: H.251, D.272, H.362, H.373, R.394, E.408, R.446 Ligands: MN.1, NA.2, GLY.3 4 PLIP interactions: 4 interactions with chain A, Hydrophobic interactions: A:H.362 Salt bridges: A:H.251, A:H.373, A:R.394 PRO.11: 9 residues within 4Å: Chain B: D.272, H.362, H.373, R.394, E.408, R.446 Ligands: MN.8, NA.9, GLY.10 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:H.362 Salt bridges: B:H.373, B:R.394 Hydrogen bonds: P.11

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: Q.24, R.31, T.86, G.87 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.31, A:R.31 Water bridges: A:Q.24, A:G.87 GOL.6: 2 residues within 4Å: Chain A: D.419, A.423 No protein-ligand interaction detected (PLIP) GOL.7: 3 residues within 4Å: Chain A: T.148, E.383, R.384 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.148, A:E.383, A:R.384, A:R.384 GOL.12: 4 residues within 4Å: Chain B: A.428, S.429, L.431, N.432 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.432 Water bridges: B:A.428, B:L.431 GOL.13: 2 residues within 4Å: Chain B: W.321, H.398 No protein-ligand interaction detected (PLIP) GOL.14: 3 residues within 4Å: Chain B: R.25, C.179, F.182 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.25 Water bridges: B:R.25 GOL.15: 2 residues within 4Å: Chain B: R.397, H.398 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.398, B:H.398 Water bridges: B:R.397, B:R.397, B:Q.400

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