SMTL ID : 4oel.2 (1 other biounit)

Crystal structure of Cathepsin C in complex with dipeptide substrates

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

hetero-4-4-mer

Ligands

4 x SER: SERINE(Non-covalent)

SER.1: 10 residues within 4Å: Chain A: D.1, C.234, Y.235, G.276, G.277, F.278 Chain B: N.10, H.11, A.12 Ligands: TYR.2 3 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain A Water bridges: S.1 Hydrogen bonds: A:D.1, A:G.277 SER.7: 10 residues within 4Å: Chain C: D.1, C.234, Y.235, G.276, G.277, F.278 Chain D: N.10, H.11, A.12 Ligands: TYR.8 3 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain C Water bridges: S.7 Hydrogen bonds: C:D.1, C:G.277 SER.13: 10 residues within 4Å: Chain E: D.1, C.234, Y.235, G.276, G.277, F.278 Chain F: N.10, H.11, A.12 Ligands: TYR.14 3 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain E Water bridges: S.13 Hydrogen bonds: E:D.1, E:G.277 SER.19: 10 residues within 4Å: Chain G: D.1, C.234, Y.235, G.276, G.277, F.278 Chain H: N.10, H.11, A.12 Ligands: TYR.20 3 PLIP interactions: 2 interactions with chain G, 1 Ligand-Ligand interactions Hydrogen bonds: G:D.1, G:G.277 Water bridges: S.19

4 x TYR: TYROSINE(Covalent)

TYR.2: 10 residues within 4Å: Chain A: D.1, Q.228, G.232, S.233, C.234, E.275, G.276 Chain B: N.10, H.11 Ligands: SER.1 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A, Hydrogen bonds: B:N.10, B:H.11, A:D.1, A:Q.228, A:C.234 TYR.8: 10 residues within 4Å: Chain C: D.1, Q.228, G.232, S.233, C.234, E.275, G.276 Chain D: N.10, H.11 Ligands: SER.7 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:D.1, C:Q.228, C:C.234, D:N.10, D:H.11 TYR.14: 10 residues within 4Å: Chain E: D.1, Q.228, G.232, S.233, C.234, E.275, G.276 Chain F: N.10, H.11 Ligands: SER.13 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain F, Hydrogen bonds: E:D.1, E:Q.228, E:C.234, F:N.10 Water bridges: E:D.1 TYR.20: 10 residues within 4Å: Chain G: D.1, Q.228, G.232, S.233, C.234, E.275, G.276 Chain H: N.10, H.11 Ligands: SER.19 5 PLIP interactions: 4 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:D.1, G:Q.228, G:C.234, H:N.10 Water bridges: G:D.1

12 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.3: 5 residues within 4Å: Chain A: N.252 Chain C: L.54 Chain G: H.206, L.207, T.209 6 PLIP interactions: 1 interactions with chain A, 4 interactions with chain G, 1 interactions with chain C Hydrogen bonds: A:N.252, G:H.206 Hydrophobic interactions: G:H.206, G:T.209, C:L.54 Water bridges: G:T.209 NAG.4: 1 residues within 4Å: Chain A: N.95 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.95 Water bridges: A:C.94 NAG.5: 4 residues within 4Å: Chain A: N.5, 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.9: 5 residues within 4Å: Chain A: L.54 Chain C: N.252 Chain E: H.206, L.207, T.209 6 PLIP interactions: 4 interactions with chain E, 1 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: E:H.206, E:T.209, A:L.54 Hydrogen bonds: E:H.206, C:N.252 Water bridges: E:T.209 NAG.10: 1 residues within 4Å: Chain C: N.95 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.95 Water bridges: C:C.94 NAG.11: 4 residues within 4Å: Chain C: N.5, N.65 Chain D: F.6, L.8 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.5, C:N.65 NAG.15: 5 residues within 4Å: Chain C: H.206, L.207, T.209 Chain E: N.252 Chain G: L.54 6 PLIP interactions: 1 interactions with chain E, 1 interactions with chain G, 4 interactions with chain C Hydrogen bonds: E:N.252, C:H.206 Hydrophobic interactions: G:L.54, C:H.206, C:T.209 Water bridges: C:T.209 NAG.16: 1 residues within 4Å: Chain E: N.95 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.95 Water bridges: E:C.94 NAG.17: 4 residues within 4Å: Chain E: N.5, N.65 Chain F: F.6, L.8 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.5, E:N.65 NAG.21: 5 residues within 4Å: Chain A: H.206, L.207, T.209 Chain E: L.54 Chain G: N.252 6 PLIP interactions: 4 interactions with chain A, 1 interactions with chain E, 1 interactions with chain G Hydrophobic interactions: A:H.206, A:T.209, E:L.54 Hydrogen bonds: A:H.206, G:N.252 Water bridges: A:T.209 NAG.22: 1 residues within 4Å: Chain G: N.95 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:N.95 Water bridges: G:C.94 NAG.23: 4 residues within 4Å: Chain G: N.5, N.65 Chain H: F.6, L.8 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:N.5, G:N.65

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

CL.6: 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.12: 6 residues within 4Å: Chain C: F.278, P.279, Y.280, Y.323 Chain D: I.59, V.61 Ligand excluded by PLIP CL.18: 6 residues within 4Å: Chain E: F.278, P.279, Y.280, Y.323 Chain F: I.59, V.61 Ligand excluded by PLIP CL.24: 6 residues within 4Å: Chain G: F.278, P.279, Y.280, Y.323 Chain H: I.59, V.61 Ligand excluded by PLIP

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: ACEG
Dipeptidyl peptidase 1 Light chain: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

G
A

B
B

D
B

F
B

H
B

Dipeptidyl peptidase 1 Heavy chain

Dipeptidyl peptidase 1 Light chain

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