SMTL ID : 6qsc.1

Crystal Structure of Arg470His mutant of Human Prolidase with Mn ions and GlyPro ligand

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 9 residues within 4Å: Chain A: D.287, H.370, H.377, T.410, E.412, E.452 Ligands: MH2.2, GLY.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, GLY.6 MN.8: 9 residues within 4Å: Chain B: D.287, H.370, H.377, T.410, E.412, E.452 Ligands: MH2.9, GLY.16, PRO.17 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.287, B:H.370, B:E.412, B:E.452

2 x MH2: MANGANESE ION, 1 HYDROXYL COORDINATED(Non-covalent)

MH2.2: 10 residues within 4Å: Chain A: Y.241, D.276, D.287, T.289, E.412, R.450, E.452 Ligands: MN.1, GLY.6, PRO.7 7 PLIP interactions: 6 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:R.450, G.6 Metal complexes: A:D.276, A:D.276, A:D.287, A:D.287, A:E.452 MH2.9: 10 residues within 4Å: Chain B: Y.241, D.276, D.287, T.289, E.412, R.450, E.452 Ligands: MN.8, GLY.16, PRO.17 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.450 Metal complexes: B:D.276, B:D.276, B:D.287, B:E.452

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: T.152, Y.382, V.386, E.387, R.388 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.152, A:R.388, A:R.388 Water bridges: A:R.388 GOL.4: 6 residues within 4Å: Chain A: E.227, R.237, H.238, S.239 Chain B: E.227, R.237 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:E.227, B:R.237, A:S.239, A:S.239, A:S.239 GOL.5: 7 residues within 4Å: Chain A: S.8, F.9, W.10, L.11, K.120 Chain B: P.262, D.264 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.8, A:W.10, B:D.264, B:D.264 Water bridges: A:K.120, A:K.120, A:Y.121 GOL.10: 5 residues within 4Å: Chain B: T.152, Y.382, V.386, E.387, R.388 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.387, B:R.388, B:R.388, B:R.388 GOL.11: 6 residues within 4Å: Chain B: L.34, R.35, V.40, A.42, V.88, D.89 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.35, B:V.40, B:D.89 Water bridges: B:G.43 GOL.12: 7 residues within 4Å: Chain B: Y.83, V.129, D.130, I.132, S.162, F.163, D.164 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.83, B:D.130, B:D.164 GOL.13: 9 residues within 4Å: Chain A: A.105, T.106 Chain B: E.249, A.252, V.253, F.417, I.418, D.419, H.420 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.419, B:D.419, A:A.105 Water bridges: B:E.249, B:D.419, B:H.420 GOL.14: 7 residues within 4Å: Chain A: P.262, D.264 Chain B: S.8, F.9, W.10, L.11, K.120 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.8, B:W.10, A:D.264 Water bridges: B:T.78, B:K.120, B:K.120, B:Y.121 GOL.15: 6 residues within 4Å: Chain B: E.14, T.15, L.16, K.17, Y.197, K.200 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.14, B:K.200

2 x GLY: GLYCINE(Non-covalent)

GLY.6: 13 residues within 4Å: Chain A: Y.241, I.244, H.255, D.276, D.287, H.370, V.376, H.377, E.412, R.450 Ligands: MN.1, MH2.2, PRO.7 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:D.276, A:H.377, G.6 GLY.16: 13 residues within 4Å: Chain B: Y.241, I.244, H.255, D.276, D.287, H.370, V.376, H.377, E.412, R.450 Ligands: MN.8, MH2.9, PRO.17 3 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain B Hydrogen bonds: G.16, B:D.276, B:H.377

2 x PRO: PROLINE(Non-covalent)

PRO.7: 16 residues within 4Å: Chain A: I.244, L.254, H.255, D.276, H.366, G.367, H.370, H.377, R.398, E.412, Y.416, R.450 Chain B: W.107 Ligands: MN.1, MH2.2, GLY.6 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:H.366 Hydrogen bonds: A:H.255 Water bridges: A:R.398 Salt bridges: A:H.255, A:H.377, A:R.398 PRO.17: 15 residues within 4Å: Chain A: W.107 Chain B: I.244, L.254, H.255, D.276, H.366, H.370, H.377, R.398, E.412, Y.416, R.450 Ligands: MN.8, MH2.9, GLY.16 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:H.366 Hydrogen bonds: B:H.255, P.17 Salt bridges: B:H.255, B:H.377, B:R.398

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Linhares, N.D. et al., Structural analysis of new compound heterozygous variants in PEPD gene identified in a patient with Prolidase Deficiency diagnosed by exome sequencing. Genet Mol Biol (2021)

Release Date

2020-03-18

Peptides

Xaa-Pro dipeptidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Xaa-Pro dipeptidase

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