SMTL ID : 4oem.1

Crystal structure of Cathepsin C in complex with dipeptide substrates

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

hetero-2-2-mer

Ligands

2 x GLY: GLYCINE(Non-covalent)

GLY.1: 8 residues within 4Å: Chain A: D.1, C.234, Y.235, G.276, G.277, F.278 Chain B: N.10 Ligands: LYS.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.277, A:G.277 GLY.12: 8 residues within 4Å: Chain C: D.1, C.234, Y.235, G.276, G.277, F.278 Chain D: N.10 Ligands: LYS.13 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.277, C:G.277

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 B, 2 interactions with chain A Hydrogen bonds: B:N.10, B:H.11, A:Q.228, A:C.234 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)

CL.7: 6 residues within 4Å: Chain A: F.278, P.279, Y.280, Y.323 Chain B: I.59, V.61 Ligand excluded by PLIP CL.18: 6 residues within 4Å: Chain C: F.278, P.279, Y.280, Y.323 Chain D: I.59, V.61 Ligand excluded by PLIP

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: 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:W.35, C:Q.228, C:A.229 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
A

C
A

B
B

D
B

Dipeptidyl peptidase 1 Heavy chain

Dipeptidyl peptidase 1 Light chain

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