SMTL ID : 7qhj.2 (1 other biounit)

Peptide GAKSAA in complex with human cathepsin V C25A mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x SER- ALA- ALA- NH2: SER-ALA-ALA-AMI(Non-covalent)

SER-ALA-ALA-NH2.1: 14 residues within 4Å: Chain A: Q.19, G.23, S.24, A.25, W.26, G.67, G.68, F.69, M.70, A.136, D.163, H.164, G.165 Ligands: MPD.5 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.26 Hydrogen bonds: A:Q.19, A:A.25, A:W.26, A:G.68, A:D.163, A:D.163, A:G.165 Water bridges: A:D.163

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

CL.2: 3 residues within 4Å: Chain A: F.69, M.70, A.71 Ligand excluded by PLIP

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: R.8, V.13, T.14, P.15, V.16, K.187, Y.199 Ligands: GOL.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.8, A:Y.199 GOL.4: 7 residues within 4Å: Chain A: D.84, S.88, Y.89, P.90, K.99, R.101, N.104 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.84, A:R.101, A:N.104 Water bridges: A:S.88 GOL.6: 6 residues within 4Å: Chain A: G.11, V.13, T.14, P.15, L.45 Ligands: GOL.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.14 Water bridges: A:R.8, A:G.11 GOL.7: 7 residues within 4Å: Chain A: T.113, V.115, K.125, A.126, T.129, V.130, Y.218 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.129 GOL.8: 7 residues within 4Å: Chain A: D.138, G.140, H.141, S.158, N.161, L.162, D.163 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.138, A:H.141, A:L.162 Water bridges: A:N.161

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

MPD.5: 7 residues within 4Å: Chain A: A.139, G.140, Q.145, D.163, H.164, W.190 Ligands: SER-ALA-ALA-NH2.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.190 Water bridges: A:Q.145, A:H.164

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
BA

Cathepsin L2

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