SMTL ID : 7q9h.1 (1 other biounit)

Peptide LLKAVAEKQ in complex with human cathepsin V C25A mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

hetero-1-2-mer

Ligands

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

CL.1: 8 residues within 4Å: Chain A: Q.19, G.23, S.24, A.25, H.164 Chain B: K.4 Chain C: A.5, V.6 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: R.8, N.197 Ligands: GOL.6 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: F.69, M.70, A.71 Ligands: MPD.8 Ligand excluded by PLIP

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

MPD.2: 9 residues within 4Å: Chain A: A.139, G.140, D.163, H.164, W.190 Chain B: K.4 Chain C: A.5, V.6 Ligands: GOL.3 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.163 Water bridges: A:H.164 Hydrophobic interactions: B:K.4 MPD.7: 4 residues within 4Å: Chain A: T.14, P.15, L.45, S.47 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.15 Water bridges: A:S.47 MPD.8: 4 residues within 4Å: Chain A: F.69, A.71, R.72 Ligands: CL.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.69, A:F.69, A:F.69

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 10 residues within 4Å: Chain A: Q.19, K.20, Q.21, C.22, G.23 Chain B: K.4 Chain C: A.5, V.6, A.7 Ligands: MPD.2 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:V.6, C:V.6, C:A.7, A:K.20 Water bridges: C:E.8, A:G.23, A:C.65 GOL.6: 8 residues within 4Å: Chain A: R.8, Y.147, L.185, S.196, Y.199, V.200, K.201 Ligands: CL.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.8, A:R.8, A:Y.147 Water bridges: A:G.150

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: A
LLKAVAEKQ Peptide: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AA

B
PAA

C
PAC

Cathepsin L2

LLKAVAEKQ Peptide

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