SMTL ID : 2djf.1

Crystal Structure of human dipeptidyl peptidase I (Cathepsin C) in complex with the inhibitor Gly-Phe-CHN2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-4-4-4-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: N.5, N.65 Chain C: F.6, L.8 Ligand excluded by PLIP NAG.2: 2 residues within 4Å: Chain A: N.95, K.117 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain A: N.29, S.31 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain B: N.46 Chain K: L.1, T.3 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain D: N.5, N.65 Chain F: F.6, L.8 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain D: N.95, K.117 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain D: N.29, S.31 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain E: N.46 Chain H: L.1, T.3 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain G: N.5, N.65 Chain I: F.6, L.8 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain G: N.95, K.117 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain G: N.29, S.31 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain E: L.1, T.3 Chain H: N.46 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain J: N.5, N.65 Chain L: F.6, L.8 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain J: N.95, K.117 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain J: N.29, S.31 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: L.1, T.3 Chain K: N.46 Ligand excluded by PLIP

4 x ACY: ACETIC ACID(Non-functional Binders)

ACY.4: 6 residues within 4Å: Chain A: S.22, G.23, K.38, Y.75 Chain F: K.68, L.69 6 PLIP interactions: 3 interactions with chain F, 3 interactions with chain A Hydrogen bonds: F:L.69, F:L.69, F:L.69, A:G.23 Hydrophobic interactions: A:Y.75 Salt bridges: A:K.38 ACY.11: 6 residues within 4Å: Chain C: K.68, L.69 Chain D: S.22, G.23, K.38, Y.75 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:Y.75 Hydrogen bonds: D:G.23, C:L.69, C:L.69, C:L.69 Salt bridges: D:K.38 ACY.18: 6 residues within 4Å: Chain G: S.22, G.23, K.38, Y.75 Chain L: K.68, L.69 5 PLIP interactions: 3 interactions with chain G, 2 interactions with chain L Hydrophobic interactions: G:Y.75 Hydrogen bonds: G:G.23, L:L.69, L:L.69 Salt bridges: G:K.38 ACY.25: 6 residues within 4Å: Chain I: K.68, L.69 Chain J: S.22, G.23, K.38, Y.75 5 PLIP interactions: 2 interactions with chain I, 3 interactions with chain J Hydrogen bonds: I:L.69, I:L.69, J:G.23 Hydrophobic interactions: J:Y.75 Salt bridges: J:K.38

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

CL.6: 6 residues within 4Å: Chain B: F.72, P.73, Y.74, Y.117 Chain C: I.59, V.61 Ligand excluded by PLIP CL.13: 6 residues within 4Å: Chain E: F.72, P.73, Y.74, Y.117 Chain F: I.59, V.61 Ligand excluded by PLIP CL.20: 6 residues within 4Å: Chain H: F.72, P.73, Y.74, Y.117 Chain I: I.59, V.61 Ligand excluded by PLIP CL.27: 6 residues within 4Å: Chain K: F.72, P.73, Y.74, Y.117 Chain L: I.59, V.61 Ligand excluded by PLIP

4 x 1ZB: N-[(1S)-1-benzyl-3-diazen-1-iumylidene-2-oxopropyl]glycinamide(Covalent)

1ZB.7: 12 residues within 4Å: Chain A: D.1 Chain B: Q.22, G.26, S.27, C.28, Y.29, E.69, G.70, G.71, F.72 Chain C: N.10, H.11 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Q.22, B:C.28, B:G.71, B:G.71, C:N.10 1ZB.14: 12 residues within 4Å: Chain D: D.1 Chain E: Q.22, G.26, S.27, C.28, Y.29, E.69, G.70, G.71, F.72 Chain F: N.10, H.11 5 PLIP interactions: 1 interactions with chain F, 4 interactions with chain E Hydrogen bonds: F:N.10, E:Q.22, E:C.28, E:G.71, E:G.71 1ZB.21: 12 residues within 4Å: Chain G: D.1 Chain H: Q.22, G.26, S.27, C.28, Y.29, E.69, G.70, G.71, F.72 Chain I: N.10, H.11 5 PLIP interactions: 4 interactions with chain H, 1 interactions with chain I Hydrogen bonds: H:Q.22, H:C.28, H:G.71, H:G.71, I:N.10 1ZB.28: 12 residues within 4Å: Chain J: D.1 Chain K: Q.22, G.26, S.27, C.28, Y.29, E.69, G.70, G.71, F.72 Chain L: N.10, H.11 5 PLIP interactions: 4 interactions with chain K, 1 interactions with chain L Hydrogen bonds: K:Q.22, K:C.28, K:G.71, K:G.71, L:N.10

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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