SMTL ID : 5fcf.1

Crystal Structure of Xaa-Pro dipeptidase from Xanthomonas campestris, phosphate and Mn bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

1 x GLY- GLY- GLY: GLY-GLY-GLY(Non-covalent)

GLY-GLY-GLY.1: 9 residues within 4Å: Chain A: H.142, R.146, A.152, I.153 Chain B: F.139, H.142, R.146, A.152, I.153 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:H.142, A:H.142, A:R.146, A:I.153, A:I.153, B:R.146, B:I.153 Water bridges: A:H.142 Salt bridges: A:H.142, B:H.142, B:R.146

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

MN.2: 7 residues within 4Å: Chain A: D.262, H.331, S.358, E.360, E.374 Ligands: MN.3, PO4.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.262, A:H.331, A:E.360, A:E.374 MN.3: 6 residues within 4Å: Chain A: D.251, D.262, T.264, E.374 Ligands: MN.2, PO4.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.251, A:D.251, A:D.262, A:E.374, H2O.1 MN.7: 6 residues within 4Å: Chain B: D.262, H.331, E.360, E.374 Ligands: MN.8, PO4.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.262, B:H.331, B:E.360, B:E.374 MN.8: 6 residues within 4Å: Chain B: D.251, D.262, T.264, E.374 Ligands: MN.7, PO4.9 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.251, B:D.251, B:D.262, B:E.374, H2O.7

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 9 residues within 4Å: Chain A: H.234, D.251, D.262, H.331, H.338, E.360, E.374 Ligands: MN.2, MN.3 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Water bridges: A:D.251, A:R.328, B:R.72, B:R.72 Salt bridges: A:H.234, A:H.331, A:H.338, A:R.372 PO4.9: 8 residues within 4Å: Chain B: D.251, D.262, H.331, H.338, E.360, E.374 Ligands: MN.7, MN.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.251 Salt bridges: B:H.331, B:H.338, B:R.372

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: E.71, R.72, W.109 Chain B: Y.342 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:L.73, B:R.328 GOL.6: 8 residues within 4Å: Chain A: W.67, S.70, R.72, V.74, P.89, F.91, E.92 Chain B: H.234 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.70, A:R.72, A:E.92 Water bridges: A:S.70, A:E.71

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.10: 7 residues within 4Å: Chain A: H.338 Chain B: W.67, S.70, E.71, R.72, V.74, E.92 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.70, B:R.72, A:H.338, A:H.338 Water bridges: A:R.328

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Are, V.N. et al., Crystal structure and biochemical investigations reveal novel mode of substrate selectivity and illuminate substrate inhibition and allostericity in a subfamily of Xaa-Pro dipeptidases. Biochim. Biophys. Acta (2017)

Release Date

2016-12-07

Peptides

Proline dipeptidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Proline dipeptidase

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