SMTL ID : 5mc1.1

Crystal Structure of Asp276Asn mutant of Human Prolidase with Mn ions and GlyPro ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 8 residues within 4Å: Chain A: D.282, H.365, T.405, E.407, E.447 Ligands: NA.2, GLY.3, PRO.4 5 PLIP interactions: 1 Ligand-Ligand interactions, 4 interactions with chain A Metal complexes: GLY.3, A:D.282, A:H.365, A:E.407, A:E.447 MN.9: 8 residues within 4Å: Chain B: D.282, H.365, T.405, E.407, E.447 Ligands: NA.10, GLY.11, PRO.12 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.11

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

NA.2: 7 residues within 4Å: Chain A: N.271, D.282, E.407, E.447 Ligands: MN.1, GLY.3, PRO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.271, A:E.447 NA.8: 1 residues within 4Å: Chain A: E.222 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.222 NA.10: 7 residues within 4Å: Chain B: N.271, D.282, E.407, E.447 Ligands: MN.9, GLY.11, PRO.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.271, B:E.447

2 x GLY: GLYCINE(Non-covalent)

GLY.3: 11 residues within 4Å: Chain A: Y.236, I.239, H.250, N.271, D.282, H.365, H.372, E.407 Ligands: MN.1, NA.2, PRO.4 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.372 GLY.11: 10 residues within 4Å: Chain B: Y.236, I.239, N.271, D.282, H.365, H.372, E.407 Ligands: MN.9, NA.10, PRO.12 2 PLIP interactions: 2 interactions with chain B Water bridges: B:H.250, B:H.372

2 x PRO: PROLINE(Non-covalent)

PRO.4: 12 residues within 4Å: Chain A: L.249, H.250, N.271, H.361, H.372, R.393, E.407, R.445 Chain B: W.102 Ligands: MN.1, NA.2, GLY.3 4 PLIP interactions: 4 interactions with chain A, Hydrophobic interactions: A:H.361 Salt bridges: A:H.250, A:H.372, A:R.393 PRO.12: 12 residues within 4Å: Chain A: W.102 Chain B: L.249, H.250, N.271, H.361, H.372, R.393, E.407, R.445 Ligands: MN.9, NA.10, GLY.11 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:H.361 Salt bridges: B:H.250, B:H.372, B:R.393 Hydrogen bonds: P.12

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: S.3, F.4, W.5, L.6, K.115 Chain B: D.259 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.3, A:W.5, B:D.259 Water bridges: A:K.115 GOL.6: 3 residues within 4Å: Chain A: A.427, S.428, R.432 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.432 Water bridges: A:S.428, A:L.430, A:L.430 GOL.7: 6 residues within 4Å: Chain A: Y.78, V.124, D.125, I.127, F.158, D.159 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.124, A:D.159 Water bridges: A:I.127 GOL.13: 6 residues within 4Å: Chain B: T.147, Y.377, V.381, E.382, R.383 Ligands: GOL.16 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.147, B:E.382, B:R.383, B:R.383 GOL.14: 6 residues within 4Å: Chain B: K.109, E.110, K.113, D.120, V.121, Q.122 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.109, B:E.110, B:V.121 Water bridges: B:E.110 GOL.15: 7 residues within 4Å: Chain A: P.257, D.259 Chain B: S.3, F.4, W.5, L.6, K.115 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.3, B:W.5 Water bridges: B:T.73 GOL.16: 5 residues within 4Å: Chain B: T.147, D.148, G.150, R.383 Ligands: GOL.13 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.393 GOL.17: 4 residues within 4Å: Chain B: R.24, R.28, C.178, F.181 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.24, B:R.28 GOL.18: 6 residues within 4Å: Chain B: S.157, F.158, D.159, G.160, I.161, S.162 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.159, B:G.160, B:I.161, B:S.162, B:S.162 GOL.19: 3 residues within 4Å: Chain B: S.129, T.132, S.133 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.129

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