SMTL ID : 6sre.1

Crystal Structure of Human Prolidase S202F variant expressed in the presence of chaperones

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.39 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 9 residues within 4Å: Chain A: D.282, H.365, H.372, T.405, E.407, E.447 Ligands: MH2.6, GLY.7, PRO.8 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.282, A:H.365, A:E.407, A:E.447, GLY.7 MN.9: 9 residues within 4Å: Chain B: D.282, H.365, H.372, T.405, E.407, E.447 Ligands: MH2.10, GLY.16, PRO.17 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.282, B:H.365, B:E.407, B:E.447

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: K.109, E.110, K.113, D.120, V.121, Q.122 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.109, A:E.110, A:E.110, A:V.121, A:Q.122, A:Q.122 Water bridges: A:K.109, A:K.113 GOL.3: 5 residues within 4Å: Chain A: T.147, Y.377, V.381, E.382, R.383 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.147, A:R.383, A:R.383 Water bridges: A:E.382, A:R.383 GOL.4: 7 residues within 4Å: Chain A: P.257, D.259 Chain B: S.3, F.4, W.5, L.6, K.115 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:W.5, B:W.5, B:K.115 Water bridges: A:D.259 GOL.5: 5 residues within 4Å: Chain A: F.158, D.159, G.160, I.161, S.162 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.159, A:I.161 GOL.11: 4 residues within 4Å: Chain B: G.344, S.345, V.346, D.347 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.344, B:V.346, B:D.347, B:D.347, B:D.347 GOL.12: 5 residues within 4Å: Chain B: T.147, Y.377, V.381, E.382, R.383 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.147, B:E.382, B:R.383, B:R.383, B:R.383 GOL.13: 5 residues within 4Å: Chain B: R.306, L.327, R.330, I.331, E.334 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.306 Water bridges: B:R.306, B:R.330 GOL.14: 3 residues within 4Å: Chain B: K.292, F.293, T.294 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.292 GOL.15: 5 residues within 4Å: Chain B: R.24, R.28, E.177, C.178, F.181 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.24, B:R.24, B:R.28

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

MH2.6: 11 residues within 4Å: Chain A: Y.236, D.271, D.282, T.284, H.365, E.407, R.445, E.447 Ligands: MN.1, GLY.7, PRO.8 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: A:D.271, A:D.271, A:D.282, A:E.447 Hydrogen bonds: G.7, G.7 MH2.10: 10 residues within 4Å: Chain B: Y.236, D.271, D.282, T.284, E.407, R.445, E.447 Ligands: MN.9, GLY.16, PRO.17 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.271, B:D.271, B:D.282, B:E.447

2 x GLY: GLYCINE(Non-covalent)

GLY.7: 13 residues within 4Å: Chain A: Y.236, I.239, H.250, D.271, D.282, H.365, V.371, H.372, E.407, R.445 Ligands: MN.1, MH2.6, PRO.8 3 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain A Hydrogen bonds: G.7, A:D.282, A:H.372 GLY.16: 13 residues within 4Å: Chain B: Y.236, I.239, H.250, D.271, D.282, H.365, V.371, H.372, E.407, R.445 Ligands: MN.9, MH2.10, PRO.17 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:D.271, B:H.372, G.16

2 x PRO: PROLINE(Non-covalent)

PRO.8: 15 residues within 4Å: Chain A: I.239, L.249, H.250, D.271, H.361, G.362, H.365, H.372, R.393, E.407, R.445 Chain B: W.102 Ligands: MN.1, MH2.6, GLY.7 5 PLIP interactions: 5 interactions with chain A, Hydrophobic interactions: A:H.361 Hydrogen bonds: A:H.250 Salt bridges: A:H.250, A:H.372, A:R.393 PRO.17: 15 residues within 4Å: Chain A: W.102 Chain B: I.239, L.249, H.250, D.271, H.361, G.362, H.365, H.372, R.393, E.407, R.445 Ligands: MN.9, MH2.10, GLY.16 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:H.361 Hydrogen bonds: B:H.250, P.17 Salt bridges: B:H.250, B:H.372, B:R.393

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wator, E. et al., Co-expression with chaperones can affect protein 3D structure as exemplified by loss-of-function variants of human prolidase. Febs Lett. (2020)

Release Date

2020-07-15

Peptides

Xaa-Pro dipeptidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Xaa-Pro dipeptidase

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