SMTL ID : 5z5o.1

Structure of Pycnonodysostosis disease related I249T mutant of human cathepsin K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

hetero-1-1-mer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: K.41, R.52, D.86, M.87, E.91, K.95, Q.141 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.86, A:K.95, A:K.95, A:Q.141 Water bridges: A:K.41 GOL.2: 6 residues within 4Å: Chain A: R.128, V.133, T.134, P.135, V.136, Y.313 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.128, A:V.136 GOL.3: 3 residues within 4Å: Chain A: A.206, M.217, Y.218 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.218 GOL.4: 6 residues within 4Å: Chain A: A.80, S.266, K.267, N.307, G.309, N.310 4 PLIP interactions: 4 interactions with chain A Water bridges: A:Y.265, A:N.307, A:G.309, A:K.311 GOL.5: 3 residues within 4Å: Chain A: N.59, T.88, S.89 No protein-ligand interaction detected (PLIP) GOL.6: 6 residues within 4Å: Chain A: P.135, V.136, K.137, N.167 Ligands: EDO.11, EDO.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.136, A:N.167 GOL.7: 3 residues within 4Å: Chain A: S.106, R.228 Ligands: EDO.20 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.106, A:R.228, A:R.228 Water bridges: A:Y.230 GOL.30: 5 residues within 4Å: Chain B: K.41, R.52, D.86, M.87 Ligands: EDO.33 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.86

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

EDO.8: 4 residues within 4Å: Chain A: Y.62, I.65, H.66, E.69 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: L.168, I.201 Chain B: T.76 Ligands: MPD.39 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: V.93, T.97, G.98, L.99, N.281 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: K.137, N.138 Ligands: GOL.6 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: K.61, S.64, I.65 Ligand excluded by PLIP EDO.13: 2 residues within 4Å: Chain A: T.30, L.34 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: V.74, H.75, Y.271, D.272, E.273 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: V.125, D.126, K.129, K.130 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: Y.43, N.44, D.48, R.52 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: D.110, C.227, R.228, R.231 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: P.135, L.165, N.167 Ligands: GOL.6 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain A: Y.127, Y.132, K.160, A.246, R.247, V.248 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain A: S.106, Y.230, E.232 Ligands: GOL.7 Ligand excluded by PLIP EDO.31: 2 residues within 4Å: Chain B: Y.43, E.49 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain B: E.25, L.28, E.57, K.61 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain B: N.44, D.48, R.52 Ligands: GOL.30 Ligand excluded by PLIP

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

SO4.21: 5 residues within 4Å: Chain A: Y.43, N.44, N.45, K.46, E.49 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.43, A:Y.43, A:E.49 SO4.34: 5 residues within 4Å: Chain A: K.161, M.335 Chain B: H.75, Y.77 Ligands: MPD.41 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.161, B:H.75 SO4.35: 3 residues within 4Å: Chain B: H.39, N.82, H.83 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.83 Salt bridges: B:H.39, B:H.83 SO4.36: 2 residues within 4Å: Chain B: T.30, H.31 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.30 Salt bridges: B:H.31 SO4.37: 4 residues within 4Å: Chain B: W.32, E.33, E.49, R.53 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.49, B:R.53

7 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.22: 5 residues within 4Å: Chain A: D.126, K.129, I.291, Q.292, H.297 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.126, A:R.128, A:K.129, A:I.291, A:I.291 Water bridges: A:S.124, A:V.125 PEG.23: 6 residues within 4Å: Chain A: D.123, K.239, K.242, K.296, R.318, N.319 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.123, A:R.318, A:R.318 PEG.24: 5 residues within 4Å: Chain A: H.83, M.96, N.138, G.140, Q.141 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.138, A:Q.141 Water bridges: A:K.41, A:K.41, A:K.41, A:H.83, A:H.83 PEG.25: 3 residues within 4Å: Chain A: S.215, C.216, P.220 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.216 PEG.26: 3 residues within 4Å: Chain A: N.45, K.46, V.47 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.45, A:K.46, A:V.47 PEG.27: 3 residues within 4Å: Chain A: T.88, E.90, Q.94 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.90, A:Q.94 PEG.38: 3 residues within 4Å: Chain A: T.162 Chain B: E.78, L.79 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.79 Water bridges: B:N.67, B:E.78, B:A.80, A:T.162

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

CL.28: 3 residues within 4Å: Chain A: G.163, K.164, L.165 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.29: 4 residues within 4Å: Chain A: Q.171, D.175, Y.207, E.214 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.171

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.39: 8 residues within 4Å: Chain A: L.154, Q.157, L.158, K.161, V.195, M.335 Chain B: T.76 Ligands: EDO.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.154, A:Q.157, A:K.161 MPD.40: 2 residues within 4Å: Chain B: K.46, V.47 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.46, B:V.47 MPD.41: 3 residues within 4Å: Chain B: V.74, H.75 Ligands: SO4.34 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roy, S. et al., Not all pycnodysostosis-related mutants of human cathepsin K are inactive - crystal structure and biochemical studies of an active mutant I249T. FEBS J. (2018)

Release Date

2018-09-26

Peptides

Cathepsin K: A
Cathepsin K: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cathepsin K

Cathepsin K