SMTL ID : 2djg.1

Re-determination of the native structure of human dipeptidyl peptidase I (cathepsin C)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-4-4-4-mer

Ligands

4 x NAG- NAG- BMA- BMA- BMA: beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA-BMA.1: 4 residues within 4Å: Chain A: Y.93, N.95, E.96, K.116 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.93 Hydrogen bonds: A:Y.93 NAG-NAG-BMA-BMA-BMA.7: 4 residues within 4Å: Chain D: Y.93, N.95, E.96, K.116 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.93 Hydrogen bonds: D:Y.93 NAG-NAG-BMA-BMA-BMA.13: 4 residues within 4Å: Chain G: Y.93, N.95, E.96, K.116 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:Y.93 NAG-NAG-BMA-BMA-BMA.19: 4 residues within 4Å: Chain J: Y.93, N.95, E.96, K.116 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:Y.93

8 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 4 residues within 4Å: Chain A: N.5, N.65 Chain C: F.6, L.8 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.6, C:L.8 Water bridges: A:N.65, A:N.65 NAG.4: 3 residues within 4Å: Chain B: N.46 Chain K: L.1, T.3 2 PLIP interactions: 1 interactions with chain K, 1 interactions with chain B Hydrophobic interactions: K:T.3 Hydrogen bonds: B:N.46 NAG.8: 4 residues within 4Å: Chain D: N.5, N.65 Chain F: F.6, L.8 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain F Water bridges: D:N.65, D:N.65 Hydrophobic interactions: F:F.6, F:L.8 NAG.10: 3 residues within 4Å: Chain E: N.46 Chain H: L.1, T.3 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain E Hydrophobic interactions: H:T.3 Hydrogen bonds: E:N.46 NAG.14: 4 residues within 4Å: Chain G: N.5, N.65 Chain I: F.6, L.8 4 PLIP interactions: 2 interactions with chain I, 2 interactions with chain G Hydrophobic interactions: I:F.6, I:L.8 Water bridges: G:N.65, G:N.65 NAG.16: 3 residues within 4Å: Chain E: L.1, T.3 Chain H: N.46 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain E Hydrogen bonds: H:N.46 Hydrophobic interactions: E:T.3 NAG.20: 4 residues within 4Å: Chain J: N.5, N.65 Chain L: F.6, L.8 4 PLIP interactions: 2 interactions with chain L, 2 interactions with chain J Hydrophobic interactions: L:F.6, L:L.8 Water bridges: J:N.65, J:N.65 NAG.22: 3 residues within 4Å: Chain B: L.1, T.3 Chain K: N.46 2 PLIP interactions: 1 interactions with chain K, 1 interactions with chain B Hydrogen bonds: K:N.46 Hydrophobic interactions: B:T.3

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 8 residues within 4Å: Chain A: S.22, G.23, Y.75, N.109, W.110, A.111 Chain E: F.108 Chain F: L.69 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:S.22, A:G.23, A:N.109, F:L.69 SO4.6: 4 residues within 4Å: Chain B: N.21 Chain C: G.36, T.37, G.38 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:N.21, C:T.37, C:G.38 SO4.9: 8 residues within 4Å: Chain B: F.108 Chain C: L.69 Chain D: S.22, G.23, Y.75, N.109, W.110, A.111 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.22, D:G.23, D:N.109, C:L.69 SO4.12: 4 residues within 4Å: Chain E: N.21 Chain F: G.36, T.37, G.38 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:N.21, F:T.37, F:G.38 SO4.15: 8 residues within 4Å: Chain G: S.22, G.23, Y.75, N.109, W.110, A.111 Chain K: F.108 Chain L: L.69 5 PLIP interactions: 4 interactions with chain G, 1 interactions with chain L Hydrogen bonds: G:S.22, G:G.23, G:Y.75, G:N.109, L:L.69 SO4.18: 4 residues within 4Å: Chain H: N.21 Chain I: G.36, T.37, G.38 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain H Hydrogen bonds: I:T.37, I:G.38, H:N.21 SO4.21: 8 residues within 4Å: Chain H: F.108 Chain I: L.69 Chain J: S.22, G.23, Y.75, N.109, W.110, A.111 5 PLIP interactions: 4 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:S.22, J:G.23, J:Y.75, J:N.109, I:L.69 SO4.24: 4 residues within 4Å: Chain K: N.21 Chain L: G.36, T.37, G.38 3 PLIP interactions: 2 interactions with chain L, 1 interactions with chain K Hydrogen bonds: L:T.37, L:G.38, K:N.21

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

CL.5: 5 residues within 4Å: Chain B: F.72, P.73, Y.74, Y.117 Chain C: V.61 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain E: F.72, P.73, Y.74, Y.117 Chain F: V.61 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain H: F.72, P.73, Y.74, Y.117 Chain I: V.61 Ligand excluded by PLIP CL.23: 5 residues within 4Å: Chain K: F.72, P.73, Y.74, Y.117 Chain L: V.61 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Molgaard, A. et al., The crystal structure of human dipeptidyl peptidase I (cathepsin C) in complex with the inhibitor Gly-Phe-CHN2. Biochem.J. (2007)

Release Date

2006-11-14

Peptides

Dipeptidyl-peptidase 1: ADGJ
Dipeptidyl-peptidase 1: BEHK
Dipeptidyl-peptidase 1: CFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

G
A

J
A

B
B

E
B

H
B

K
B

C
C

F
C

I
C

L
C

Dipeptidyl-peptidase 1

Dipeptidyl-peptidase 1

Dipeptidyl-peptidase 1

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