SMTL ID : 4r60.1

Crystal Structure of Xaa-Pro dipeptidase from Xanthomonas campestris

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 6 residues within 4Å: Chain A: H.143, R.147, A.153, I.154 Chain B: F.140, H.143 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Salt bridges: B:H.143, A:H.143, A:R.147 Hydrogen bonds: A:I.154

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

MN.2: 5 residues within 4Å: Chain A: D.252, D.263, T.265, E.375 Ligands: MN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.252, A:D.252, A:D.263, A:E.375 MN.3: 5 residues within 4Å: Chain A: D.263, H.332, E.361, E.375 Ligands: MN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.263, A:H.332, A:E.361, A:E.375 MN.4: 5 residues within 4Å: Chain B: D.263, H.332, E.361, E.375 Ligands: MN.5 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.263, B:H.332, B:E.361, B:E.375 MN.5: 5 residues within 4Å: Chain B: D.252, D.263, T.265, E.375 Ligands: MN.4 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.252, B:D.252, B:D.263, B:E.375, H2O.20

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

NA.6: 6 residues within 4Å: Chain B: Q.47, D.156, A.157, G.158, A.159, I.160 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.47, B:A.157, B:A.159, B:I.160 Water bridges: B:D.156 NA.7: 3 residues within 4Å: Chain B: V.204, S.220, C.223 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.220, B:C.223

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, A. et al., Crystal Structure of Xaa-Pro dipeptidase from Xanthomonas campestris. to be published

Release Date

2014-09-17

Peptides

Proline dipeptidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Proline dipeptidase