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

Peptide VYEKKP in complex with human cathepsin V C25S mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

2 x VAL- TYR- GLU- LYS- LYS- PRO: VAL-TYR-GLU-LYS-LYS-PRO(Non-covalent)

VAL-TYR-GLU-LYS-LYS-PRO.1: 14 residues within 4Å: Chain A: S.144, F.147, Y.148, K.149, S.150, G.151, I.152, Y.153, F.154, E.155, E.194, W.195, G.196, N.198 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.148 Hydrogen bonds: A:F.147, A:K.149, A:S.150, A:S.150, A:S.150, A:I.152, A:G.196 Water bridges: A:F.154, A:E.155 Salt bridges: A:K.149, A:K.149 VAL-TYR-GLU-LYS-LYS-PRO.2: 19 residues within 4Å: Chain A: Q.20, G.24, S.25, S.26, W.27, Q.64, C.66, N.67, G.68, G.69, F.70, M.71, A.137, L.163, D.164, H.165, G.166, A.216 Ligands: CL.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.26, A:C.66, A:G.69, A:G.69, A:D.164, A:H.165 Water bridges: A:Q.20 pi-Stacking: A:F.70

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

CL.3: 4 residues within 4Å: Chain A: F.70, M.71, A.72 Ligands: VAL-TYR-GLU.2 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: R.73 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: Q.180, N.181, K.183, D.206, K.207 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.206, A:K.207 Water bridges: A:K.183, A:K.205

2 x TFA: trifluoroacetic acid(Non-covalent)

TFA.5: 7 residues within 4Å: Chain A: E.121, K.122, M.125, K.183, W.185, K.205, D.206 7 PLIP interactions: 7 interactions with chain A Water bridges: A:K.122, A:Q.180, A:K.183, A:K.183 Salt bridges: A:K.122, A:K.183, A:K.205 TFA.7: 6 residues within 4Å: Chain A: R.9, L.186, S.197, N.198, Y.200, K.202 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.197, A:S.197, A:N.198 Salt bridges: A:R.9

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

MPD.6: 8 residues within 4Å: Chain A: T.114, V.116, A.117, K.126, A.127, T.130, V.131, Y.219 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.116, A:K.126, A:V.131, A:Y.219 Water bridges: A:A.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Loboda, J. et al., Peptide VYEKKP in complex with human cathepsin V C25S mutant. To Be Published

Release Date

2023-01-18

Peptides

Cathepsin L2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AA

Cathepsin L2

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