SMTL ID : 3ee6.1 (1 other biounit)

Crystal Structure Analysis of Tripeptidyl peptidase -I

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: R.208, N.210, F.516, N.552 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.210 NAG.2: 5 residues within 4Å: Chain A: G.217, S.218, G.219, A.252, N.286 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.286 Hydrogen bonds: A:N.286 NAG.3: 2 residues within 4Å: Chain A: S.113, N.313 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.313 NAG.4: 3 residues within 4Å: Chain A: N.414, N.443, S.445 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.443 Hydrogen bonds: A:N.443, A:S.445 NAG.12: 4 residues within 4Å: Chain B: R.208, N.210, F.516, N.552 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.210 NAG.13: 5 residues within 4Å: Chain B: G.217, G.219, A.252, Q.254, N.286 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.286 NAG.14: 3 residues within 4Å: Chain B: H.112, S.113, N.313 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.313 NAG.15: 3 residues within 4Å: Chain B: Q.373, N.414, N.443 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:N.443 Hydrogen bonds: B:Q.373, B:N.443

8 x ZN: ZINC ION(Non-covalent)

ZN.5: 3 residues within 4Å: Chain A: H.197, D.457 Chain B: E.529 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Metal complexes: B:E.529, A:H.197, A:D.457, A:D.457 ZN.6: 2 residues within 4Å: Chain A: E.137, H.155 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.137, A:E.137, A:H.155 ZN.7: 3 residues within 4Å: Chain A: E.45, H.140, H.149 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.45, A:H.149 ZN.8: 2 residues within 4Å: Chain A: E.424, H.511 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.424, A:E.424, A:H.511 ZN.16: 2 residues within 4Å: Chain B: E.137, H.155 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.137, B:E.137, B:H.155 ZN.17: 3 residues within 4Å: Chain A: E.529 Chain B: H.197, D.457 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:H.197, B:D.457, A:E.529, A:E.529 ZN.18: 3 residues within 4Å: Chain B: E.45, H.140, H.149 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.45, B:H.140, B:H.149 ZN.19: 2 residues within 4Å: Chain B: E.424, H.511 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.424, B:E.424, B:H.511, H2O.3

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 6 residues within 4Å: Chain A: R.492, R.497, R.506, N.562, P.563, R.564 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain B: R.492, R.497, R.506, P.563, R.564 Ligand excluded by PLIP

2 x CA: CALCIUM ION(Non-covalent)

CA.10: 6 residues within 4Å: Chain A: D.517, V.518, G.539, G.541, D.543, T.546 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.517, A:V.518, A:G.539, A:G.541, A:D.543, H2O.2 CA.21: 6 residues within 4Å: Chain B: D.517, V.518, G.539, P.540, G.541, D.543 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.517, B:V.518, B:G.539, B:G.541, B:D.543, H2O.3

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.11: 2 residues within 4Å: Chain A: R.28, R.375 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.28, A:R.375 SO4.22: 2 residues within 4Å: Chain B: R.28, R.375 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.28, B:R.375

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pal, A. et al., Structure of tripeptidyl-peptidase I provides insight into the molecular basis of late infantile neuronal ceroid lipofuscinosis. J.Biol.Chem. (2009)

Release Date

2008-11-25

Peptides

Tripeptidyl-peptidase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tripeptidyl-peptidase 1

Related Entries With Identical Sequence