SMTL ID : 4oel.1 (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-2-2-mer

Ligands

2 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: 2 interactions with chain C, 1 Ligand-Ligand interactions Hydrogen bonds: C:D.1, C:G.277 Water bridges: S.7

2 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: 3 interactions with chain A, 2 interactions with chain B, Hydrogen bonds: A:D.1, A:Q.228, A:C.234, B:N.10, B:H.11 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

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

NAG.3: 2 residues within 4Å: Chain A: N.252 Chain C: L.54 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.54 Hydrogen bonds: A:N.252 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: 2 residues within 4Å: Chain A: L.54 Chain C: N.252 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.54 Hydrogen bonds: C:N.252 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

2 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

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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