SMTL ID : 6qsb.1

Crystal Structure of Arg470His mutant of Human Prolidase with Mn ions

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: D.287, H.370, T.410, E.412, E.452 Ligands: MN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.287, A:H.370, A:E.412, A:E.452 MN.2: 7 residues within 4Å: Chain A: Y.241, D.276, D.287, T.289, R.450, E.452 Ligands: MN.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.276, A:D.276, A:D.287, A:E.452, H2O.13 MN.6: 6 residues within 4Å: Chain B: D.287, H.370, T.410, E.412, E.452 Ligands: MN.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.287, B:H.370, B:E.412, B:E.452 MN.7: 7 residues within 4Å: Chain B: Y.241, D.276, D.287, T.289, R.450, E.452 Ligands: MN.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.276, B:D.276, B:D.287, B:E.452, H2O.27

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: M.210, K.211, V.213, K.214, C.478, M.479, A.480, G.481 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.213 Water bridges: A:V.213, A:V.213 GOL.4: 7 residues within 4Å: Chain A: W.325, G.385, V.386, E.387, I.389, A.400, H.402 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.387, A:E.387 GOL.5: 5 residues within 4Å: Chain A: T.152, Y.382, V.386, E.387, R.388 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.388, A:R.388, A:R.388 GOL.8: 8 residues within 4Å: Chain B: L.310, S.313, R.314, M.317, I.451, E.453, H.470, T.471 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.313, B:S.313 GOL.9: 7 residues within 4Å: Chain B: E.249, A.252, V.253, F.417, I.418, D.419, G.445 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.419, B:G.445 Water bridges: B:H.420 GOL.10: 7 residues within 4Å: Chain A: P.262, D.264 Chain B: S.8, F.9, W.10, L.11, K.120 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.8, B:W.10, A:D.264 GOL.11: 6 residues within 4Å: Chain B: S.162, F.163, D.164, G.165, I.166, S.167 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.164, B:G.165, B:I.166, B:S.167 Water bridges: B:S.162, B:F.163

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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