SMTL ID : 2hu5.1

Binding of inhibitors by Acylaminoacyl-peptidase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x GLY: GLYCINE(Non-covalent)

GLY.1: 4 residues within 4Å: Chain A: G.369, F.485, R.526 Ligands: PHE.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:R.526, F.2 Water bridges: A:G.369, A:F.371 GLY.6: 4 residues within 4Å: Chain B: G.369, F.485, R.526 Ligands: PHE.7 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:R.526, F.7

2 x PHE: PHENYLALANINE(Non-covalent)

PHE.2: 13 residues within 4Å: Chain A: G.368, G.369, S.445, Y.446, W.474, M.477, F.485, F.488, I.489, R.526, T.527, H.556 Ligands: GLY.1 11 PLIP interactions: 10 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:W.474, A:F.485, A:F.488, A:I.489, A:T.527 Hydrogen bonds: A:G.369, A:G.369, A:S.445, A:Y.446, G.1 Salt bridges: A:H.556 PHE.7: 11 residues within 4Å: Chain B: G.368, G.369, S.445, Y.446, W.474, M.477, F.485, F.488, R.526, T.527 Ligands: GLY.6 11 PLIP interactions: 10 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:W.474, B:F.485, B:F.485, B:F.488, B:T.527 Hydrogen bonds: B:G.369, B:G.369, B:S.445, B:Y.446, G.6 Salt bridges: B:H.556

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: L.163, T.179, S.180, N.181, R.188, P.225, R.226 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.179, A:T.179, A:P.225, A:R.226, A:R.226 GOL.4: 1 residues within 4Å: Chain A: F.155 No protein-ligand interaction detected (PLIP) GOL.5: 8 residues within 4Å: Chain A: R.76, K.94, L.106, E.122, A.123, V.124, L.139, D.140 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.76, A:R.76, A:K.94, A:V.124 GOL.8: 6 residues within 4Å: Chain B: Y.478, E.490, T.493, G.495, R.497, M.500 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.493, B:T.493, B:G.495, B:R.497 GOL.9: 7 residues within 4Å: Chain B: R.76, K.94, L.106, E.122, A.123, L.139, D.140 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.76, B:R.76, B:K.94, B:E.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kiss, A.L. et al., The Acylaminoacyl Peptidase from Aeropyrum pernix K1 Thought to Be an Exopeptidase Displays Endopeptidase Activity. J.Mol.Biol. (2007)

Release Date

2007-05-15

Peptides

Acylamino-acid-releasing enzyme: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Acylamino-acid-releasing enzyme

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