SMTL ID : 6jd0.1

Structure of mutant human cathepsin L, engineered for GAG binding

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: M.85, H.89, E.92, H.98, F.100, M.102, E.281, S.282 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.281 Water bridges: A:E.281, A:S.282 GOL.2: 7 residues within 4Å: Chain A: Y.139, W.147, Y.152, R.180, A.267, T.268 Ligands: GOL.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.180, A:R.180, A:A.267 GOL.3: 7 residues within 4Å: Chain A: K.131, V.132, F.133, Q.134, P.136, V.253, Y.357 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.134, A:Q.134, A:Q.134 GOL.4: 9 residues within 4Å: Chain A: Y.139, P.142, V.145, D.146, W.147, K.150, A.267, T.268 Ligands: GOL.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.139, A:A.267 GOL.5: 8 residues within 4Å: Chain A: M.178, T.182, R.184, I.186, V.246, A.247, N.248 Ligands: GOL.10 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.182, A:R.184, A:R.184, A:V.246, A:N.248 GOL.6: 7 residues within 4Å: Chain A: R.148, V.153, T.154, P.155, V.156, K.326, Y.338 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.154, A:Y.338 Water bridges: A:V.156, A:V.156 GOL.7: 9 residues within 4Å: Chain A: N.124, R.125, K.126, P.127, R.128, Y.209, D.211, Y.212, L.354 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.126, A:K.126, A:D.211 Water bridges: A:D.211, A:Y.212, A:S.356 GOL.8: 4 residues within 4Å: Chain A: E.227, S.228, P.230 Ligands: PGE.41 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.228 GOL.9: 5 residues within 4Å: Chain A: P.142, R.143, S.144, F.312 Ligands: EDO.50 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.143, A:S.144, A:S.144 GOL.10: 7 residues within 4Å: Chain A: G.221, G.222, S.245, V.246, A.247, N.248 Ligands: GOL.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.221, A:N.248 GOL.11: 7 residues within 4Å: Chain A: R.148, L.324, N.335, K.336, Y.338, K.340 Ligands: PGE.43 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.148, A:R.148, A:N.335 Water bridges: A:D.146 GOL.12: 4 residues within 4Å: Chain A: G.68, M.69, N.70, E.71 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.68, A:G.68, A:M.69, A:N.70, A:N.70, A:E.71 GOL.13: 2 residues within 4Å: Chain A: R.346 Ligands: PO4.27 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.346, A:R.346 GOL.14: 5 residues within 4Å: Chain A: E.135, P.136, L.137, F.138, Y.139 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.137, A:F.138, A:Y.139

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

CL.15: 3 residues within 4Å: Chain A: L.185 Ligands: NA.18, POL.38 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain A: K.149 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain A: P.256, K.257, Q.258 Ligand excluded by PLIP

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

NA.18: 5 residues within 4Å: Chain A: G.151, F.179, L.185 Ligands: CL.15, POL.38 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.151 NA.19: 7 residues within 4Å: Chain A: V.156, K.157, N.158, G.330, E.331 Ligands: PO4.28, POL.35 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.157 Water bridges: A:V.156 NA.20: 4 residues within 4Å: Chain A: E.288 Ligands: NA.22, PO4.24, PO4.25 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.288 NA.21: 4 residues within 4Å: Chain A: E.87, Q.91, R.94 Ligands: PO4.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.87, A:R.94 NA.22: 5 residues within 4Å: Chain A: T.101, K.287, E.288 Ligands: NA.20, PO4.25 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.101, A:E.288, A:E.288

8 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.23: 7 residues within 4Å: Chain A: I.86, E.87, N.90, R.94 Ligands: NA.21, PO4.25, POL.31 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.87, A:N.90 Salt bridges: A:R.94 PO4.24: 2 residues within 4Å: Chain A: K.287 Ligands: NA.20 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.287 Salt bridges: A:K.287 PO4.25: 7 residues within 4Å: Chain A: N.90, Y.93, R.94, T.101 Ligands: NA.20, NA.22, PO4.23 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.94 PO4.26: 4 residues within 4Å: Chain A: R.116, Q.117, C.205, N.206 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.205, A:N.206 Water bridges: A:G.163 Salt bridges: A:R.116 PO4.27: 5 residues within 4Å: Chain A: F.292, R.345, R.346 Ligands: GOL.13, PGE.42 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.345, A:R.346 PO4.28: 6 residues within 4Å: Chain A: N.158, G.330, E.331, E.332 Ligands: NA.19, POL.35 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.158, A:E.331, A:E.332 PO4.29: 4 residues within 4Å: Chain A: R.125, P.127, R.128, K.257 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.128 Salt bridges: A:R.125, A:R.128, A:K.257 PO4.30: 3 residues within 4Å: Chain A: T.182, G.183, R.184 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.182, A:G.183, A:R.184

10 x POL: N-PROPANOL(Non-covalent)

POL.31: 7 residues within 4Å: Chain A: Q.55, M.83, I.86, E.87, A.103, M.104 Ligands: PO4.23 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.103, A:M.104 POL.32: 8 residues within 4Å: Chain A: V.78, K.81, N.82, M.85, M.110, F.115, E.281, F.285 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.78 Hydrogen bonds: A:N.82, A:N.82, A:E.281 POL.33: 5 residues within 4Å: Chain A: K.257, S.298, E.299, N.347, S.353 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.347 Hydrogen bonds: A:E.299 POL.34: 6 residues within 4Å: Chain A: F.115, R.116, M.119, G.279, H.280, L.284 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.115 POL.35: 7 residues within 4Å: Chain A: K.157, N.158, F.168, Y.231 Ligands: NA.19, PO4.28, PGE.46 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.157, A:Y.231 Hydrogen bonds: A:N.158 POL.36: 1 residues within 4Å: Chain A: L.66 No protein-ligand interaction detected (PLIP) POL.37: 8 residues within 4Å: Chain A: K.129, G.130, K.131, Q.215, Q.218, T.250, G.251, F.252 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.252 Hydrogen bonds: A:K.131, A:K.131, A:F.252 POL.38: 7 residues within 4Å: Chain A: F.179, G.183, R.184, L.185, I.186 Ligands: CL.15, NA.18 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.184 Hydrogen bonds: A:L.185 POL.39: 15 residues within 4Å: Chain A: V.118, M.119, N.120, G.121, Q.159, C.162, G.163, S.164, S.165, W.166, G.207, D.302, H.303, A.304, W.329 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.120 Hydrogen bonds: A:S.165, A:D.302 POL.40: 5 residues within 4Å: Chain A: T.154, P.155, K.157, S.187, E.226 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.187

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

PGE.41: 7 residues within 4Å: Chain A: S.228, Y.229, P.230, K.239, N.241, Y.244 Ligands: GOL.8 No protein-ligand interaction detected (PLIP) PGE.42: 10 residues within 4Å: Chain A: S.99, I.290, F.292, N.319, N.320, K.321, A.342, K.343, R.345 Ligands: PO4.27 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.319, A:K.321, A:K.321, A:R.345, A:R.345 Water bridges: A:N.320 PGE.43: 11 residues within 4Å: Chain A: Y.286, K.287, E.288, G.289, I.290, E.313, N.335, Y.338, V.339, K.340 Ligands: GOL.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.286, A:G.289, A:K.340, A:K.340 PGE.44: 6 residues within 4Å: Chain A: L.46, T.47, F.48, H.50, R.76 Ligands: EDO.51 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.48, A:H.50 Water bridges: A:E.53, A:R.76 PGE.45: 5 residues within 4Å: Chain A: K.126, K.129, Q.200, G.201, Y.212 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.126, A:K.129 PGE.46: 8 residues within 4Å: Chain A: N.158, Q.159, G.160, Q.161, Y.231, E.232, A.233 Ligands: POL.35 No protein-ligand interaction detected (PLIP)

3 x EOH: ETHANOL(Non-functional Binders)

EOH.47: 6 residues within 4Å: Chain A: D.277, H.280, D.295, C.296, S.297, D.300 4 PLIP interactions: 4 interactions with chain A Water bridges: A:D.277, A:D.277, A:D.300, A:D.302 EOH.48: 6 residues within 4Å: Chain A: K.60, A.61, R.65, L.66, Y.67, E.72 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.66 EOH.49: 9 residues within 4Å: Chain A: V.194, D.195, C.196, S.197, G.198, N.202, E.203, G.204, E.235 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.195 Water bridges: A:G.198

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

EDO.50: 9 residues within 4Å: Chain A: S.144, V.145, D.146, Y.310, G.311, F.312, Y.322, L.324 Ligands: GOL.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.145, A:V.145, A:F.312, A:Y.322 Water bridges: A:D.146 EDO.51: 8 residues within 4Å: Chain A: F.48, H.50, W.56, K.60, E.72, G.73, R.76 Ligands: PGE.44 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.56, A:E.72, A:R.76

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