SMTL ID : 7qo2.1

Peptide GAKSAA in complex with human cathepsin V C25A mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-dimer

Ligands

1 x GLY- ALA- LYS: GAKSAA Peptide(Non-covalent)

GLY-ALA-LYS.1: 15 residues within 4Å: Chain A: Q.20, G.24, S.25, A.26, W.27, N.67, G.68, G.69, F.70, A.137, D.164, H.165, G.166 Ligands: MPD.3, CL.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.20, A:A.26, A:G.69, A:G.69, A:D.164 Water bridges: A:W.27, A:H.165, A:G.166

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

MPD.2: 7 residues within 4Å: Chain A: A.140, G.141, H.142, Q.146, D.164, H.165, W.191 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.191 Hydrogen bonds: A:A.140, A:D.164 Water bridges: A:Q.146, A:H.165 MPD.3: 12 residues within 4Å: Chain A: W.27, G.68, G.69, F.70, M.71, A.137, L.163, D.164, H.165 Ligands: GLY-ALA-LYS.1, GLY-ALA-LYS.1, GLY-ALA-LYS.1 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.70 Hydrogen bonds: A:G.69 MPD.7: 6 residues within 4Å: Chain A: Y.13, F.40, R.41, K.42, T.43, G.44 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.40 MPD.8: 6 residues within 4Å: Chain B: A.140, G.141, Q.146, D.164, H.165, W.191 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.191 Hydrogen bonds: B:A.140, B:D.164 Water bridges: B:H.142 MPD.13: 8 residues within 4Å: Chain A: T.15, P.16, L.46, S.48 Chain B: K.11, G.12, F.40, G.44 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.15, A:P.16, A:L.46

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

CL.4: 7 residues within 4Å: Chain A: Q.20, G.24, S.25, A.26, W.27, H.165 Ligands: GLY-ALA-LYS.1 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: F.70, M.71, A.72 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain B: F.70, M.71, A.72 Ligands: GOL.11 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: T.114, V.116, K.126, A.127, T.130, V.131, Y.219 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.130, A:T.130 GOL.11: 7 residues within 4Å: Chain B: A.72, F.113, V.115, A.216, A.217, S.218 Ligands: CL.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.217 Water bridges: B:S.218 GOL.12: 4 residues within 4Å: Chain B: C.23, G.24, C.66, N.67 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.24

1 x TFA: trifluoroacetic acid(Non-covalent)

TFA.10: 5 residues within 4Å: Chain A: K.4, S.5, F.174 Chain B: P.91, V.93 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.5, A:S.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Loboda, J. et al., Peptide GAKSAA in complex with human cathepsin V C25A mutant. To Be Published

Release Date

2023-01-18

Peptides

Cathepsin L2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AA

B
BA

Cathepsin L2

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