SMTL ID : 3ee6.2 (1 other biounit)

Crystal Structure Analysis of Tripeptidyl peptidase -I

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-tetramer

Ligands

16 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 Ligand excluded by PLIP NAG.2: 5 residues within 4Å: Chain A: G.217, S.218, G.219, A.252, N.286 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain A: S.113, N.313 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: N.414, N.443, S.445 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain B: R.208, N.210, F.516, N.552 Ligand excluded by PLIP NAG.13: 5 residues within 4Å: Chain B: G.217, G.219, A.252, Q.254, N.286 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain B: H.112, S.113, N.313 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain B: Q.373, N.414, N.443 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain C: R.208, N.210, F.516, N.552 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain C: G.217, S.218, G.219, A.252, N.286 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain C: S.113, N.313 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain C: N.414, N.443, S.445 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain D: R.208, N.210, F.516, N.552 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain D: G.217, G.219, A.252, Q.254, N.286 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain D: H.112, S.113, N.313 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain D: Q.373, N.414, N.443 Ligand excluded by PLIP

16 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: 3 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.197, A:D.457, A:D.457, B:E.529 ZN.6: 5 residues within 4Å: Chain A: E.137, H.155 Chain C: E.137, H.155 Ligands: ZN.28 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Metal complexes: A:E.137, A:E.137, A:H.155, C:H.155 ZN.7: 4 residues within 4Å: Chain A: E.45, H.140, H.149 Chain D: E.147 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Metal complexes: A:E.45, A:H.149, D:E.147, D:E.147 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: 5 residues within 4Å: Chain B: E.137, H.155 Chain D: E.137, H.155 Ligands: ZN.38 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain B Metal complexes: D:H.155, 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 A, 2 interactions with chain B Metal complexes: A:E.529, A:E.529, B:H.197, B:D.457 ZN.18: 4 residues within 4Å: Chain B: E.45, H.140, H.149 Chain C: E.147 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Metal complexes: B:E.45, B:H.140, B:H.149, C:E.147 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 ZN.27: 3 residues within 4Å: Chain C: H.197, D.457 Chain D: E.529 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Metal complexes: C:H.197, C:D.457, C:D.457, D:E.529 ZN.28: 5 residues within 4Å: Chain A: E.137, H.155 Chain C: E.137, H.155 Ligands: ZN.6 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Metal complexes: C:E.137, C:E.137, C:H.155, A:H.155 ZN.29: 4 residues within 4Å: Chain B: E.147 Chain C: E.45, H.140, H.149 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Metal complexes: B:E.147, B:E.147, C:E.45, C:H.149 ZN.30: 2 residues within 4Å: Chain C: E.424, H.511 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.424, C:E.424, C:H.511 ZN.38: 5 residues within 4Å: Chain B: E.137, H.155 Chain D: E.137, H.155 Ligands: ZN.16 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Metal complexes: D:E.137, D:E.137, D:H.155, B:H.155 ZN.39: 3 residues within 4Å: Chain C: E.529 Chain D: H.197, D.457 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Metal complexes: D:H.197, D:D.457, C:E.529, C:E.529 ZN.40: 4 residues within 4Å: Chain A: E.147 Chain D: E.45, H.140, H.149 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Metal complexes: D:E.45, D:H.140, D:H.149, A:E.147 ZN.41: 2 residues within 4Å: Chain D: E.424, H.511 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.424, D:E.424, D:H.511, H2O.6

4 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 CL.31: 6 residues within 4Å: Chain C: R.492, R.497, R.506, N.562, P.563, R.564 Ligand excluded by PLIP CL.42: 5 residues within 4Å: Chain D: R.492, R.497, R.506, P.563, R.564 Ligand excluded by PLIP

4 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 CA.32: 6 residues within 4Å: Chain C: D.517, V.518, G.539, G.541, D.543, T.546 6 PLIP interactions: 5 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.517, C:V.518, C:G.539, C:G.541, C:D.543, H2O.4 CA.43: 6 residues within 4Å: Chain D: D.517, V.518, G.539, P.540, G.541, D.543 6 PLIP interactions: 5 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.517, D:V.518, D:G.539, D:G.541, D:D.543, H2O.6

4 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 SO4.33: 2 residues within 4Å: Chain C: R.28, R.375 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:R.28, C:R.375 SO4.44: 2 residues within 4Å: Chain D: R.28, R.375 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:R.28, D: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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Tripeptidyl-peptidase 1

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