SMTL ID : 2qs8.2 (3 other biounits)

Crystal structure of a Xaa-Pro dipeptidase with bound methionine in the active site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: H.69, H.71, K.194, D.328 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.69, A:H.71, A:D.328, H2O.6 MG.3: 4 residues within 4Å: Chain B: H.69, H.71, K.194, D.328 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.69, B:H.71, B:D.328, H2O.11 MG.5: 4 residues within 4Å: Chain C: H.69, H.71, K.194, D.328 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.69, C:H.71, C:D.328, H2O.16 MG.7: 4 residues within 4Å: Chain D: H.69, H.71, K.194, D.328 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.69, D:H.71, D:D.328, H2O.21

4 x MET: METHIONINE(Non-covalent)

MET.2: 12 residues within 4Å: Chain A: H.150, G.200, V.201, L.202, H.235, H.237, H.255, T.277, A.280, G.281, I.309, D.328 9 PLIP interactions: 7 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:V.201, A:L.202, A:D.328, M.2, M.2 Water bridges: A:H.235 Salt bridges: A:H.150, A:H.235, A:H.237 MET.4: 12 residues within 4Å: Chain B: H.150, G.200, V.201, L.202, H.235, H.237, H.255, T.277, A.280, G.281, I.309, D.328 9 PLIP interactions: 7 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:V.201, B:L.202, B:D.328, M.4, M.4 Water bridges: B:H.235 Salt bridges: B:H.150, B:H.235, B:H.237 MET.6: 12 residues within 4Å: Chain C: H.150, G.200, V.201, L.202, H.235, H.237, H.255, T.277, A.280, G.281, I.309, D.328 9 PLIP interactions: 7 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: C:V.201, C:L.202, C:D.328, M.6, M.6 Water bridges: C:H.235 Salt bridges: C:H.150, C:H.235, C:H.237 MET.8: 12 residues within 4Å: Chain D: H.150, G.200, V.201, L.202, H.235, H.237, H.255, T.277, A.280, G.281, I.309, D.328 9 PLIP interactions: 7 interactions with chain D, 2 Ligand-Ligand interactions Hydrogen bonds: D:V.201, D:L.202, D:D.328, M.8, M.8 Water bridges: D:H.235 Salt bridges: D:H.150, D:H.235, D:H.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiang, D.F. et al., Functional annotation of two new carboxypeptidases from the amidohydrolase superfamily of enzymes. Biochemistry (2009)

Release Date

2007-08-21

Peptides

Xaa-Pro Dipeptidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

D
B

Xaa-Pro Dipeptidase

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