- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.52 Å
- Oligo State
- hetero-2-2-mer
- Ligands
- 2 x GLY: GLYCINE(Non-covalent)
- 2 x LYS: LYSINE(Covalent)
LYS.2: 13 residues within 4Å:- Chain A: D.1, Q.228, G.232, S.233, C.234, Y.235, E.275, G.276
- Chain B: N.10, H.11, A.12
- Ligands: GLY.1, EDO.8
4 PLIP interactions:2 interactions with chain A, 2 interactions with chain B- Hydrogen bonds: A:Q.228, A:C.234, B:N.10, B:H.11
LYS.13: 13 residues within 4Å:- Chain C: D.1, Q.228, G.232, S.233, C.234, Y.235, E.275, G.276
- Chain D: N.10, H.11, A.12
- Ligands: GLY.12, EDO.19
4 PLIP interactions:2 interactions with chain D, 2 interactions with chain C,- Hydrogen bonds: D:N.10, D:H.11, C:Q.228, C:C.234
- 2 x SO4: SULFATE ION(Non-functional Binders)
SO4.3: 5 residues within 4Å:- Chain A: D.304, S.305, P.306, C.307
- Ligands: EDO.10
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:S.305
- Water bridges: A:C.307
SO4.14: 5 residues within 4Å:- Chain C: D.304, S.305, P.306, C.307
- Ligands: EDO.21
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:S.305
- Water bridges: C:C.307
- 6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)
NAG.4: 4 residues within 4Å:- Chain A: I.219, N.252
- Chain C: L.54
- Ligands: NAG.5
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:N.252
NAG.5: 2 residues within 4Å:- Chain A: I.219
- Ligands: NAG.4
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:I.219
NAG.6: 5 residues within 4Å:- Chain A: N.5, Y.64, N.65
- Chain B: F.6, L.8
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:N.5, A:N.65
NAG.15: 4 residues within 4Å:- Chain A: L.54
- Chain C: I.219, N.252
- Ligands: NAG.16
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:N.252
NAG.16: 2 residues within 4Å:- Chain C: I.219
- Ligands: NAG.15
1 PLIP interactions:1 interactions with chain C- Hydrophobic interactions: C:I.219
NAG.17: 5 residues within 4Å:- Chain C: N.5, Y.64, N.65
- Chain D: F.6, L.8
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:N.5, C:N.65
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- 8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.8: 7 residues within 4Å:- Chain A: Q.228, A.229, S.230, C.231
- Chain B: H.11, W.35
- Ligands: LYS.2
3 PLIP interactions:1 interactions with chain B, 2 interactions with chain A- Hydrogen bonds: B:W.35, A:Q.228, A:A.229
EDO.9: 9 residues within 4Å:- Chain A: V.28, W.101, W.110, C.267, S.268, Q.269, Y.270, Y.286, F.290
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:C.267, A:Q.269
- Water bridges: A:V.28, A:V.28, A:W.101
EDO.10: 9 residues within 4Å:- Chain A: V.265, S.266, C.267, S.268, Q.269, A.271, Q.272, G.273
- Ligands: SO4.3
1 PLIP interactions:1 interactions with chain A- Water bridges: A:S.268
EDO.11: 10 residues within 4Å:- Chain A: D.48, H.59, F.60, T.61, E.69, I.70, V.71, Y.280, G.326, F.327
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:H.59, A:V.71
- Water bridges: A:F.60, A:G.326
EDO.19: 7 residues within 4Å:- Chain C: Q.228, A.229, S.230, C.231
- Chain D: H.11, W.35
- Ligands: LYS.13
3 PLIP interactions:2 interactions with chain C, 1 interactions with chain D- Hydrogen bonds: C:Q.228, C:A.229, D:W.35
EDO.20: 9 residues within 4Å:- Chain C: V.28, W.101, W.110, C.267, S.268, Q.269, Y.270, Y.286, F.290
5 PLIP interactions:5 interactions with chain C- Hydrogen bonds: C:C.267, C:Q.269
- Water bridges: C:V.28, C:V.28, C:W.101
EDO.21: 9 residues within 4Å:- Chain C: V.265, S.266, C.267, S.268, Q.269, A.271, Q.272, G.273
- Ligands: SO4.14
1 PLIP interactions:1 interactions with chain C- Water bridges: C:S.268
EDO.22: 10 residues within 4Å:- Chain C: D.48, H.59, F.60, T.61, E.69, I.70, V.71, Y.280, G.326, F.327
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:H.59, C:V.71
- Water bridges: C:F.60, C:G.326
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Rubach, J.K. et al., The amino-acid substituents of dipeptide substrates of cathepsin C can determine the rate-limiting steps of catalysis. Biochemistry (2012)
- Release Date
- 2015-03-25
- Peptides
- Dipeptidyl peptidase 1 Heavy chain: AC
Dipeptidyl peptidase 1 Light chain: BD - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AC
AB
BD
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.52 Å
- Oligo State
- hetero-2-2-mer
- Ligands
- 2 x GLY: GLYCINE(Non-covalent)
- 2 x LYS: LYSINE(Covalent)
- 2 x SO4: SULFATE ION(Non-functional Binders)
- 6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- 8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Rubach, J.K. et al., The amino-acid substituents of dipeptide substrates of cathepsin C can determine the rate-limiting steps of catalysis. Biochemistry (2012)
- Release Date
- 2015-03-25
- Peptides
- Dipeptidyl peptidase 1 Heavy chain: AC
Dipeptidyl peptidase 1 Light chain: BD - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AC
AB
BD
B