SMTL ID : 7q9c.2 (1 other biounit)

Peptide RLSAKP 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 LEU- SER- ALA- LYS- PRO- NH2: RLSAKP Peptide(Non-covalent)

LEU-SER-ALA-LYS-PRO-NH2.1: 21 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 Ligands: MPD.3, MPD.4, CL.5, MPD.10 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.69, A:F.69 Hydrogen bonds: A:Q.19, A:A.25, A:W.26, A:G.68, A:G.68, A:D.163, A:G.165

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

MPD.2: 9 residues within 4Å: Chain A: N.18, Q.19, K.20, Q.21, Q.145, W.190, W.194 Ligands: MPD.3, MPD.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.190, A:W.190 Water bridges: A:Q.145 MPD.3: 9 residues within 4Å: Chain A: A.139, G.140, Q.145, D.163, H.164, W.190 Ligands: LEU-SER-ALA-LYS-PRO-NH2.1, LEU-SER-ALA-LYS-PRO-NH2.1, MPD.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.190 MPD.4: 8 residues within 4Å: Chain A: Q.19, K.20, Q.21, C.22, G.23 Ligands: LEU-SER-ALA-LYS-PRO-NH2.1, MPD.2, MPD.7 No protein-ligand interaction detected (PLIP) MPD.7: 6 residues within 4Å: Chain A: Q.21, C.22, G.23, C.65, N.66 Ligands: MPD.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.21, A:G.23, A:C.65 MPD.9: 4 residues within 4Å: Chain A: R.58, D.95, E.96, I.97 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.97 Water bridges: A:R.58, A:D.95 MPD.10: 8 residues within 4Å: Chain A: A.71, F.112, V.114, A.215, S.217 Ligands: LEU-SER-ALA-LYS-PRO-NH2.1, LEU-SER-ALA-LYS-PRO-NH2.1, CL.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.112, A:V.114

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

CL.5: 5 residues within 4Å: Chain A: F.69, M.70, A.71 Ligands: LEU-SER-ALA-LYS-PRO-NH2.1, MPD.10 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: D.84, S.88, Y.89, P.90, K.99, R.101, N.104 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.84, A:R.101, A:N.104 Water bridges: A:R.101, A:R.101 GOL.8: 7 residues within 4Å: Chain A: R.8, V.13, T.14, P.15, V.16, K.187, Y.199 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.13, A:V.16, A:Y.199

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

Human cathepsin V: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
BA

Human cathepsin V

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