SMTL ID : 6h2p.1

Crystal Structure of Arg184Gln mutant of Human Prolidase with Mn ions and Cacodylate ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 7 residues within 4Å: Chain A: D.287, H.370, T.410, E.412, E.452 Ligands: MN.2, CAC.3 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, E.452 Ligands: MN.1, CAC.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.276, A:D.276, A:D.287, A:E.452 MN.7: 7 residues within 4Å: Chain B: D.287, H.370, T.410, E.412, E.452 Ligands: MN.8, CAC.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.287, B:H.370, B:E.412, B:E.452 MN.8: 7 residues within 4Å: Chain B: Y.241, D.276, D.287, T.289, E.452 Ligands: MN.7, CAC.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.276, B:D.276, B:D.287, B:E.452

2 x CAC: CACODYLATE ION(Non-covalent)

CAC.3: 13 residues within 4Å: Chain A: Y.241, I.244, D.276, D.287, H.370, V.376, H.377, R.398, E.412, R.450, E.452 Ligands: MN.1, MN.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.377 Water bridges: A:R.398 CAC.9: 14 residues within 4Å: Chain B: Y.241, I.244, H.255, D.276, D.287, H.370, V.376, H.377, R.398, E.412, R.450, E.452 Ligands: MN.7, MN.8 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.377 Water bridges: B:H.255, B:R.398, B:R.398, B:E.412

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: H.255, H.366, G.367, S.396, R.398 Chain B: W.107 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.255, A:S.396, A:R.398 GOL.5: 10 residues within 4Å: Chain A: Q.49, G.50, G.51, E.52, E.68, L.147, R.159, E.160, A.161 Chain B: Y.57 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.50, A:R.159 Water bridges: A:Q.49, A:Q.49, A:E.52, A:L.147, A:R.159 GOL.6: 7 residues within 4Å: Chain A: S.8, F.9, W.10, L.11, K.120 Chain B: P.262, D.264 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.8, A:W.10, B:D.264 Water bridges: A:T.78, A:K.120 GOL.10: 9 residues within 4Å: Chain A: Y.57 Chain B: Q.49, G.50, G.51, E.68, L.147, R.159, E.160, A.161 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.159, B:R.159 Water bridges: B:Q.49, B:Q.49, B:E.52, B:R.159, B:S.162 GOL.11: 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:W.10, A:D.264 Water bridges: B:K.120

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

2018-08-29

Peptides

Xaa-Pro dipeptidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Xaa-Pro dipeptidase