SMTL ID : 5x49.1

Crystal Structure of Human mitochondrial X-prolyl Aminopeptidase (XPNPEP3)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

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

MN.1: 7 residues within 4Å: Chain A: D.291, H.373, T.398, E.400, E.424 Ligands: MN.2, 01B.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.291, A:H.373, A:E.400, A:E.424 MN.2: 8 residues within 4Å: Chain A: Y.249, D.280, D.291, T.293, E.400, E.424 Ligands: MN.1, 01B.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.280, A:D.280, A:D.291, A:E.424 MN.9: 7 residues within 4Å: Chain B: D.291, H.373, T.398, E.400, E.424 Ligands: MN.10, 01B.12 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.291, B:H.373, B:E.400, B:E.424, 01B.12 MN.10: 8 residues within 4Å: Chain B: Y.249, D.280, D.291, T.293, E.400, E.424 Ligands: MN.9, 01B.12 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.280, B:D.280, B:D.291, B:E.424

2 x 12P: DODECAETHYLENE GLYCOL(Non-covalent)

12P.3: 11 residues within 4Å: Chain A: L.23, R.24, K.27, Y.72, R.191, L.192, I.195, M.385, L.389, Q.392 Ligands: DMS.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.27, A:R.191, A:R.191 12P.11: 11 residues within 4Å: Chain B: L.23, R.24, K.27, Y.72, R.191, L.192, L.194, I.195, L.389, Q.392 Ligands: DMS.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.27, B:R.191

2 x 01B: (2S,3R)-3-amino-2-hydroxy-4-phenylbutanoic acid(Non-covalent)

01B.4: 17 residues within 4Å: Chain A: Y.249, P.250, V.252, H.263, V.265, D.280, D.291, H.373, H.380, E.400, E.424 Chain B: I.60, P.61 Ligands: MN.1, MN.2, DMS.5, DMS.7 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.60, B:I.60, A:Y.249, A:V.252, A:V.265 Salt bridges: A:H.373, A:H.380 01B.12: 17 residues within 4Å: Chain A: I.60, P.61 Chain B: Y.249, P.250, V.252, H.263, V.265, D.280, D.291, H.373, H.380, E.400, E.424 Ligands: MN.9, MN.10, DMS.13, DMS.15 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.249, B:V.252, B:V.265, A:I.60, A:I.60 Water bridges: B:H.263 Salt bridges: B:H.373, B:H.380

6 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 8 residues within 4Å: Chain A: L.262, H.263, H.369, E.400, R.422 Chain B: W.112 Ligands: 01B.4, DMS.7 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.422 DMS.6: 4 residues within 4Å: Chain A: V.19, E.20, L.23 Ligands: 12P.3 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.20 DMS.7: 8 residues within 4Å: Chain A: H.369, H.370, G.372, H.373, R.387, E.400 Ligands: 01B.4, DMS.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.370 Salt bridges: A:E.400 DMS.13: 8 residues within 4Å: Chain A: W.112 Chain B: L.262, H.263, H.369, E.400, R.422 Ligands: 01B.12, DMS.15 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.422 DMS.14: 4 residues within 4Å: Chain B: V.19, E.20, L.23 Ligands: 12P.11 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.20 DMS.15: 7 residues within 4Å: Chain B: H.370, G.372, H.373, R.387, E.400 Ligands: 01B.12, DMS.13 3 PLIP interactions: 3 interactions with chain B Water bridges: B:H.370, B:R.387 Salt bridges: B:E.400

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 3 residues within 4Å: Chain A: L.247, Y.249 Chain B: M.56 No protein-ligand interaction detected (PLIP) EDO.16: 4 residues within 4Å: Chain A: M.56 Chain B: I.246, L.247, Y.249 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, R. et al., Structure of the human aminopeptidase XPNPEP3 and comparison of its in vitro activity with Icp55 orthologs: Insights into diverse cellular processes. J. Biol. Chem. (2017)

Release Date

2017-05-17

Peptides

Probable Xaa-Pro aminopeptidase 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Probable Xaa-Pro aminopeptidase 3