SMTL ID : 3edy.1

Crystal Structure of the Precursor Form of Human Tripeptidyl-Peptidase 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.498, V.499, G.520, G.522, D.524 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.498, A:V.499, A:G.520, A:G.522, A:D.524, H2O.2

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 8 residues within 4Å: Chain A: R.189, Y.190, N.191, E.383, F.497, T.531, P.532, N.533 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.190, A:F.497 Hydrogen bonds: A:R.189, A:R.189 Water bridges: A:R.189 NAG.3: 6 residues within 4Å: Chain A: V.197, G.198, S.199, A.233, Q.235, N.267 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.197, A:A.233 Hydrogen bonds: A:Q.235, A:N.267 NAG.4: 6 residues within 4Å: Chain A: H.93, S.94, V.95, M.290, L.291, N.294 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:H.93, A:V.95 Hydrogen bonds: A:S.94, A:N.294 NAG.5: 8 residues within 4Å: Chain A: S.394, N.395, V.396, F.397, P.398, N.424, S.426, G.427 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.397

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

EDO.6: 5 residues within 4Å: Chain A: Q.47, Y.365, P.400, Y.402, F.483 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.47 Water bridges: A:S.401, A:S.401, A:S.401 EDO.7: 5 residues within 4Å: Chain A: E.310, D.311, L.313, S.315, V.396 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.310, A:L.313 EDO.8: 6 residues within 4Å: Chain A: Q.354, N.395, S.421, Y.422, F.423, N.424 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.422, A:N.424 Water bridges: A:N.395 EDO.9: 6 residues within 4Å: Chain A: Y.60, H.300, R.331, G.332, L.333, P.480 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.300

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guhaniyogi, J. et al., Crystal Structure and Autoactivation Pathway of the Precursor Form of Human Tripeptidyl-peptidase 1, the Enzyme Deficient in Late Infantile Ceroid Lipofuscinosis. J.Biol.Chem. (2009)

Release Date

2008-11-18

Peptides

Tripeptidyl-peptidase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Tripeptidyl-peptidase 1