SMTL ID : 7q8h.1

Peptide EVCKKKK in complex with human cathepsin V C25A mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x GLU- VAL- CYS- LYS- LYS- LYS- LYS- NH2: EVCKKKK Peptide(Non-covalent)

GLU-VAL-CYS-LYS-LYS-LYS-LYS-NH2.1: 22 residues within 4Å: Chain A: Q.19, G.23, S.24, A.25, W.26, Q.63, N.66, G.67, G.68, F.69, M.70, A.136, M.137, K.160, N.161, L.162, D.163, H.164, G.165, A.215 Ligands: MPD.4, MPD.6 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:Q.19, A:A.25, A:W.26, A:Q.63, A:Q.63, A:N.66, A:G.68, A:G.68, A:N.161, A:N.161, A:L.162, A:D.163, A:D.163 Water bridges: A:N.66, A:L.162, A:L.162, A:D.163, A:D.163, A:D.163 GLU-VAL-CYS-LYS-LYS-LYS-LYS-NH2.2: 19 residues within 4Å: Chain B: Q.19, G.23, S.24, A.25, W.26, Q.63, N.66, G.67, G.68, F.69, M.70, A.136, N.161, L.162, D.163, H.164, G.165 Ligands: MPD.9, TFA.14 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:Q.19, B:A.25, B:W.26, B:Q.63, B:Q.63, B:N.66, B:G.68, B:G.68, B:N.161, B:N.161, B:L.162, B:D.163, B:D.163 Water bridges: B:L.162, B:L.162, B:D.163

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

MPD.3: 9 residues within 4Å: Chain A: N.18, Q.19, K.20, Q.21, Q.145, W.190, W.194 Ligands: MPD.4, MPD.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.190, A:W.190 Water bridges: A:Q.21 MPD.4: 10 residues within 4Å: Chain A: A.139, G.140, Q.145, D.163, H.164, W.190 Ligands: GLU-VAL-CYS-LYS-LYS-LYS-LYS-NH2.1, GLU-VAL-CYS-LYS-LYS-LYS-LYS-NH2.1, MPD.3, MPD.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:H.164 Hydrogen bonds: A:A.139, A:Q.145, A:D.163 MPD.6: 9 residues within 4Å: Chain A: Q.19, K.20, Q.21, C.22, G.23, W.190 Ligands: GLU-VAL-CYS-LYS-LYS-LYS-LYS-NH2.1, MPD.3, MPD.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.19, A:K.20, A:C.22 MPD.9: 10 residues within 4Å: Chain B: A.139, G.140, F.144, Q.145, D.163, H.164, W.190 Ligands: CYS-LYS-LYS-LYS-LYS-NH2.2, CYS-LYS-LYS-LYS-LYS-NH2.2, MPD.10 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.190 Water bridges: B:A.139, B:H.141 MPD.10: 8 residues within 4Å: Chain B: N.18, Q.19, K.20, Q.21, Q.145, W.190, W.194 Ligands: MPD.9 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Q.145, B:W.190 Water bridges: B:Q.145

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

CL.5: 3 residues within 4Å: Chain A: F.69, M.70, A.71 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: S.4, V.5, D.6, K.9, K.10 Chain B: E.87 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.6 GOL.11: 8 residues within 4Å: Chain B: D.84, S.88, Y.89, P.90, K.99, Y.100, R.101, N.104 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.84, B:R.101, B:N.104

4 x TFA: trifluoroacetic acid(Non-covalent)

TFA.8: 7 residues within 4Å: Chain A: E.120, K.121, M.124, K.182, W.184, K.204, D.205 6 PLIP interactions: 6 interactions with chain A Water bridges: A:K.121, A:K.182, A:K.182 Salt bridges: A:K.121, A:K.182, A:K.204 TFA.12: 5 residues within 4Å: Chain A: K.3, S.4, F.173 Chain B: P.90, V.92 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.4 TFA.13: 5 residues within 4Å: Chain B: P.59, Q.60, Y.76, E.79, N.80 2 PLIP interactions: 2 interactions with chain B Halogen bonds: B:E.79, B:N.80 TFA.14: 8 residues within 4Å: Chain B: F.69, M.70, A.71, A.136, A.215, S.217 Ligands: CYS-LYS-LYS-LYS-LYS-NH2.2, CYS-LYS-LYS-LYS-LYS-NH2.2 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.71, B:S.217

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tusar, L. et al., Proteomic data and structure analysis combined reveal interplay of structural rigidity and flexibility on selectivity of cysteine cathepsins. Commun Biol (2023)

Release Date

2022-11-23

Peptides

Cathepsin L2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AA

B
BA

Cathepsin L2

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