SMTL ID : 6jd8.1

Structure of a proline specific mutant of human cathepsin L

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

monomer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: F.179, G.183, R.184, L.185 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.183, A:L.185

12 x EOH: ETHANOL(Non-functional Binders)

EOH.2: 5 residues within 4Å: Chain A: E.259, D.344, R.345, R.346, N.347 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.344 EOH.3: 7 residues within 4Å: Chain A: G.121, E.203, N.206, G.207, G.208, Y.209 Ligands: PGE.16 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.209 Hydrogen bonds: A:N.206 EOH.4: 2 residues within 4Å: Chain A: L.137, F.138 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.138 EOH.5: 3 residues within 4Å: Chain A: K.131, V.253, T.359 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.359 EOH.6: 6 residues within 4Å: Chain A: Q.159, G.160, Q.161, Y.231, A.233 Ligands: EDO.15 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.233 Hydrogen bonds: A:Q.161 EOH.7: 6 residues within 4Å: Chain A: V.194, G.198, N.202, E.203, G.204, E.235 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.204, A:E.235 Water bridges: A:G.198 EOH.8: 7 residues within 4Å: Chain A: N.82, M.85, M.110, S.112, E.281, L.284, F.285 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.281, A:F.285 Hydrogen bonds: A:S.112 EOH.9: 5 residues within 4Å: Chain A: C.196, Y.216, C.238, K.239, Y.240 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.240 Hydrogen bonds: A:Y.240 EOH.10: 4 residues within 4Å: Chain A: T.45, L.46, T.47, F.48 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.48 EOH.11: 6 residues within 4Å: Chain A: E.53, W.56, T.57, K.60, E.72, R.76 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.56, A:R.76 EOH.12: 6 residues within 4Å: Chain A: T.154, P.155, K.157, S.187, E.226 Ligands: EOH.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.157, A:S.187, A:E.226 Water bridges: A:E.226 EOH.13: 7 residues within 4Å: Chain A: K.157, N.158, F.168, E.190, E.226, Y.231 Ligands: EOH.12 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.157 Hydrogen bonds: A:E.190 Water bridges: A:E.190, A:Y.231

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

PEG.14: 6 residues within 4Å: Chain A: K.181, Q.218, N.248, D.249, T.250, V.360 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.249 Water bridges: A:K.181, A:D.249

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

EDO.15: 5 residues within 4Å: Chain A: N.158, Y.231, E.232, A.233 Ligands: EOH.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.231

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.16: 19 residues within 4Å: Chain A: V.118, M.119, N.120, G.121, F.122, Q.159, C.162, G.163, S.164, S.165, W.166, G.207, G.208, Y.209, D.302, H.303, A.304, W.329 Ligands: EOH.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.165, A:D.302, A:H.303

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Choudhury, D. et al., Structure-guided protein engineering of human cathepsin L for efficient collagenolytic activity. Protein Eng.Des.Sel. (2021)

Release Date

2020-02-05

Peptides

Cathepsin L1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cathepsin L1