SMTL ID : 8v57.1

Complex of murine cathepsin K with bound cystatin C inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

hetero-2-2-mer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain A: A.88, N.101, T.103, A.104 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain B: N.101, T.103, A.104 No protein-ligand interaction detected (PLIP)

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 3 residues within 4Å: Chain A: Y.76, Q.79, N.80 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.79

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

SO4.4: 5 residues within 4Å: Chain A: N.20, G.187, E.188, S.189 Chain D: K.107 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:N.20, A:E.188, A:S.189, A:S.189 Salt bridges: D:K.107 SO4.5: 1 residues within 4Å: Chain A: N.119 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.119 SO4.6: 4 residues within 4Å: Chain A: K.124, K.178, R.200, N.201 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.124, A:R.200 SO4.7: 3 residues within 4Å: Chain A: P.4, D.5, S.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.5, A:D.5, A:S.6 SO4.8: 5 residues within 4Å: Chain B: N.20, G.187, E.188, S.189 Chain C: K.107 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain B Salt bridges: C:K.107 Hydrogen bonds: B:N.20, B:E.188, B:S.189, B:S.189, B:S.189 SO4.9: 6 residues within 4Å: Chain A: K.12, Y.14, K.41, G.45 Chain B: K.105, K.108 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Salt bridges: B:K.105, B:K.108, A:K.41 Hydrogen bonds: A:Y.14 SO4.10: 9 residues within 4Å: Chain B: T.16, K.19, F.30, A.33, G.34, E.37, L.167, K.183, S.185 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.30, B:G.34 Salt bridges: B:K.183 SO4.11: 4 residues within 4Å: Chain B: K.121, K.124, R.200, N.201 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.201 Salt bridges: B:K.121, B:K.124, B:R.200 SO4.12: 4 residues within 4Å: Chain B: T.173, Q.174, K.175, G.176 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.173, B:K.175, B:G.176 SO4.13: 7 residues within 4Å: Chain B: F.146 Chain C: G.22, R.25, Y.62, S.103, P.105, H.110 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.62, C:S.103 Salt bridges: C:R.25, C:H.110 SO4.14: 3 residues within 4Å: Chain C: P.13, R.53, F.63 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, X. et al., Heparan sulfate selectively inhibits the collagenase activity of cathepsin K. Matrix Biol. (2024)

Release Date

2024-10-09

Peptides

Cathepsin K: AB
Cystatin-C: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Cathepsin K

Cystatin-C

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