SMTL ID : 7qff.1

Peptide VACKSSQP in complex with human cathepsin V C25A mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-2-2-mer

Ligands

1 x GLU- TYR- SER: GLU-TYR-SER(Non-covalent)

GLU-TYR-SER.1: 24 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, L.162, D.163, H.164, G.165, A.215 Chain C: X.1, V.2, A.3, C.4, K.5 Ligands: CL.5, MPD.8 21 PLIP interactions: 8 interactions with chain C, 13 interactions with chain A Hydrophobic interactions: C:A.3, C:C.4, C:K.5, A:F.69, A:F.69 Hydrogen bonds: C:C.4, C:C.4, C:K.5, C:K.5, A:Q.19, A:G.23, A:A.25, A:N.66, A:G.68, A:G.68, A:G.68, A:D.163, A:H.164 Water bridges: C:A.3, A:G.165, A:G.165

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

MPD.2: 5 residues within 4Å: Chain A: K.17, N.18, F.28, E.86, Y.91 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.28, A:E.86, A:Y.91 Hydrogen bonds: A:N.18 Water bridges: A:Y.91 MPD.3: 9 residues within 4Å: Chain A: T.14, P.15, L.45, V.46, S.47 Chain B: K.10, G.11, F.39, G.43 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.15 Water bridges: A:S.47, A:S.47 MPD.4: 6 residues within 4Å: Chain A: Y.12, F.39, R.40, K.41, T.42, G.43 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.39 MPD.8: 9 residues within 4Å: Chain A: A.139, G.140, F.144, D.163, H.164, W.190 Chain C: K.5 Ligands: GLU-TYR-SER.1, GOL.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.190, A:W.190 MPD.10: 6 residues within 4Å: Chain B: A.139, G.140, D.163, H.164, W.190 Chain D: K.5 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Water bridges: D:K.5, B:H.164 MPD.12: 5 residues within 4Å: Chain B: P.59, Q.60, Y.76, E.79, N.80 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:N.80 Hydrogen bonds: B:Q.60 Water bridges: B:C.56

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

CL.5: 5 residues within 4Å: Chain A: F.69, M.70, A.71, S.217 Ligands: GLU-TYR-SER.1 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: F.69, M.70, A.71 Ligands: GOL.13 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: Q.37, R.40, K.41, V.221 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.37, A:R.40 Water bridges: A:Q.37, A:R.40, A:V.221 GOL.7: 3 residues within 4Å: Chain A: F.69, A.71, R.72 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.72 GOL.9: 6 residues within 4Å: Chain A: Q.19, Q.21, C.22, G.23, W.190 Ligands: MPD.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.21 Water bridges: A:G.23, A:C.65, A:W.190 GOL.13: 7 residues within 4Å: Chain B: A.71, F.112, V.114, A.215, A.216, S.217 Ligands: CL.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.215 Water bridges: B:S.217

1 x TFA: trifluoroacetic acid(Non-covalent)

TFA.14: 5 residues within 4Å: Chain A: K.3, F.173 Chain B: P.90, Y.91, V.92 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.91

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

2022-12-21

Peptides

Cathepsin L2: AB
ACE-VAL-ALA-CYS-LYS: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AA

B
BA

C
PA

D
PB

Cathepsin L2

ACE-VAL-ALA-CYS-LYS

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