SMTL ID : 2qs8.3 (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-octamer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: H.69, H.71, D.328 Ligands: MET.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.69, A:H.71, A:D.328, H2O.3 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, D.328 Ligands: MET.6 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.69, C:H.71, C:D.328, H2O.14 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.22 MG.9: 4 residues within 4Å: Chain E: H.69, H.71, D.328 Ligands: MET.10 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.69, E:H.71, E:D.328, H2O.25 MG.11: 4 residues within 4Å: Chain F: H.69, H.71, K.194, D.328 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.69, F:H.71, F:D.328, H2O.33 MG.13: 4 residues within 4Å: Chain G: H.69, H.71, D.328 Ligands: MET.14 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:H.69, G:H.71, G:D.328, H2O.36 MG.15: 4 residues within 4Å: Chain H: H.69, H.71, K.194, D.328 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:H.69, H:H.71, H:D.328, H2O.44

8 x MET: METHIONINE(Non-covalent)

MET.2: 13 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 Ligands: MG.1 8 PLIP interactions: 6 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:V.201, A:L.202, A:D.328, M.2, M.2 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: 13 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 Ligands: MG.5 8 PLIP interactions: 6 interactions with chain C, 2 Ligand-Ligand interactions Hydrogen bonds: C:V.201, C:L.202, C:D.328, M.6, M.6 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 MET.10: 13 residues within 4Å: Chain E: H.150, G.200, V.201, L.202, H.235, H.237, H.255, T.277, A.280, G.281, I.309, D.328 Ligands: MG.9 8 PLIP interactions: 6 interactions with chain E, 2 Ligand-Ligand interactions Hydrogen bonds: E:V.201, E:L.202, E:D.328, M.10, M.10 Salt bridges: E:H.150, E:H.235, E:H.237 MET.12: 12 residues within 4Å: Chain F: 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 F, 2 Ligand-Ligand interactions Hydrogen bonds: F:V.201, F:L.202, F:D.328, M.12, M.12 Water bridges: F:H.235 Salt bridges: F:H.150, F:H.235, F:H.237 MET.14: 13 residues within 4Å: Chain G: H.150, G.200, V.201, L.202, H.235, H.237, H.255, T.277, A.280, G.281, I.309, D.328 Ligands: MG.13 8 PLIP interactions: 6 interactions with chain G, 2 Ligand-Ligand interactions Hydrogen bonds: G:V.201, G:L.202, G:D.328, M.14, M.14 Salt bridges: G:H.150, G:H.235, G:H.237 MET.16: 12 residues within 4Å: Chain H: 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: 2 Ligand-Ligand interactions, 7 interactions with chain H Hydrogen bonds: M.16, M.16, H:V.201, H:L.202, H:D.328 Water bridges: H:H.235 Salt bridges: H:H.150, H:H.235, H: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: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

Xaa-Pro Dipeptidase

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