SMTL ID : 3c9e.1

Crystal structure of the cathepsin K : chondroitin sulfate complex.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x BDP- ASG- BDP- ASG- BDP- ASG: 2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid

BDP-ASG-BDP-ASG-BDP-ASG.1: 12 residues within 4Å: Chain A: S.4, V.5, D.6, R.8, K.9, K.10, G.170, I.171, Q.172, N.190, K.191, L.195 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.6, A:K.9 Water bridges: A:S.4, A:S.4, A:S.4 Salt bridges: A:K.10, A:K.9 BDP-ASG-BDP-ASG-BDP-ASG.4: 12 residues within 4Å: Chain B: S.4, V.5, D.6, R.8, K.9, K.10, G.170, I.171, Q.172, N.190, K.191, L.195 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.6, B:K.9 Water bridges: B:S.4, B:S.4, B:S.4 Salt bridges: B:K.10, B:K.9

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 7 residues within 4Å: Chain A: E.59, N.70, Q.73 Chain B: E.59, N.70, Q.73 Ligands: CA.5 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:E.59, B:E.59, A:E.59, A:E.59 CA.5: 7 residues within 4Å: Chain A: E.59, N.70, Q.73 Chain B: E.59, N.70, Q.73 Ligands: CA.2 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:E.59, B:E.59, A:E.59, A:E.59

2 x E64: N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE(Covalent)

E64.3: 18 residues within 4Å: Chain A: Q.19, G.23, S.24, C.25, W.26, E.59, N.60, D.61, G.65, G.66, Y.67, N.70, A.134, L.160, N.161, H.162, L.209 Chain B: Y.67 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.134, A:L.160, A:L.209 Hydrogen bonds: A:Q.19, A:G.23, A:C.25, A:E.59, A:N.60, A:G.66, A:G.66, A:N.70, A:N.161 Salt bridges: A:H.162 E64.6: 18 residues within 4Å: Chain A: Y.67 Chain B: Q.19, G.23, S.24, C.25, W.26, E.59, N.60, D.61, G.65, G.66, Y.67, N.70, A.134, L.160, N.161, H.162, L.209 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:A.134, B:L.160, B:L.209 Hydrogen bonds: B:Q.19, B:G.23, B:C.25, B:E.59, B:N.60, B:G.66, B:G.66, B:N.70, B:N.161 Salt bridges: B:H.162

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Z. et al., The crystal and molecular structures of a cathepsin K:chondroitin sulfate complex. J.Mol.Biol. (2008)

Release Date

2008-08-26

Peptides

Cathepsin K: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cathepsin K

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