SMTL ID : 7q8f.1 (1 other biounit)

Peptide GNYKEAKK in complex with human cathepsin V C25A mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

hetero-1-1-mer

Ligands

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

MPD.1: 10 residues within 4Å: Chain A: A.139, G.140, H.141, Q.145, D.163, H.164, W.190 Chain B: K.9, X.10 Ligands: GOL.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.139, A:H.164 MPD.2: 5 residues within 4Å: Chain A: K.17, N.18, F.28, E.86, Y.91 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:K.17, A:F.28, A:E.86, A:Y.91 Hydrogen bonds: A:N.18 Water bridges: A:V.16, A:Y.91 MPD.4: 5 residues within 4Å: Chain A: T.14, P.15, L.45, V.46, S.47 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.14, A:P.15 Water bridges: A:S.47 MPD.5: 8 residues within 4Å: Chain A: N.18, Q.19, K.20, Q.21, Q.145, W.190, W.194 Ligands: GOL.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.190, A:W.190 Hydrogen bonds: A:K.20

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

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

1 x TFA: trifluoroacetic acid(Non-covalent)

TFA.6: 6 residues within 4Å: Chain A: R.8, L.185, S.196, N.197, Y.199, K.201 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.196, A:N.197 Salt bridges: A:R.8

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain A: T.113, V.115, K.125, A.126, T.129, V.130, Y.218 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.129, A:T.129 Water bridges: A:V.114, A:A.126 GOL.8: 8 residues within 4Å: Chain A: Q.19, K.20, Q.21, C.22, G.23, W.190 Ligands: MPD.1, MPD.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.19, A:K.20, A:C.22, A:W.190

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
GNYKEAKK Peptide: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AA

B
PA

Cathepsin L2

GNYKEAKK Peptide

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