SMTL ID : 3ctz.1

Structure of human cytosolic X-prolyl aminopeptidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: D.426, H.489, E.523, E.537 Ligands: MN.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.426, A:H.489, A:E.523, H2O.1, H2O.35 MN.2: 6 residues within 4Å: Chain A: F.381, D.415, D.426, T.428, E.537 Ligands: MN.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.415, A:D.426, A:E.537, H2O.1, H2O.35 MN.6: 5 residues within 4Å: Chain B: D.426, H.489, E.523, E.537 Ligands: MN.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.426, B:H.489, B:E.523, H2O.42, H2O.75 MN.7: 6 residues within 4Å: Chain B: F.381, D.415, D.426, T.428, E.537 Ligands: MN.6 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.415, B:D.426, B:E.537, H2O.42, H2O.75

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 1 residues within 4Å: Chain A: T.435 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.435, A:T.435, H2O.2, H2O.4, H2O.5 CA.8: 1 residues within 4Å: Chain B: T.435 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.435, B:T.435, H2O.43, H2O.44, H2O.45

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

NA.4: 4 residues within 4Å: Chain A: H.485, G.486, K.507 Ligands: P6G.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.486, A:K.507 NA.9: 4 residues within 4Å: Chain B: H.485, G.486, K.507 Ligands: P6G.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.486, B:K.507

2 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.5: 10 residues within 4Å: Chain A: F.381, I.384, I.394, H.395, H.485, G.486, H.489, H.498, E.523 Ligands: NA.4 No protein-ligand interaction detected (PLIP) P6G.10: 10 residues within 4Å: Chain B: F.381, I.384, I.394, H.395, H.485, G.486, H.489, H.498, E.523 Ligands: NA.9 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, X. et al., Structure of human cytosolic X-prolyl aminopeptidase: a double Mn(II)-dependent dimeric enzyme with a novel three-domain subunit. J.Biol.Chem. (2008)

Release Date

2008-05-27

Peptides

Xaa-Pro aminopeptidase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Xaa-Pro aminopeptidase 1