SMTL ID : 7q9c.1 (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

2 x ARG- LEU- SER: RLSAKP Peptide(Non-covalent)

ARG-LEU-SER.1: 20 residues within 4Å: Chain A: Q.19, G.23, A.25, W.26, N.66, G.67, G.68, F.69, M.70, A.136, M.137, L.162, D.163, H.164, G.165 Ligands: ALA-LYS-PRO-NH2.2, ALA-LYS-PRO-NH2.2, CL.3, MPD.4, MPD.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.66, A:G.68, A:G.68, A:D.163, A:H.164 Water bridges: A:A.25 ARG-LEU-SER.2: 17 residues within 4Å: Chain A: N.18, Q.19, K.20, Q.21, C.22, G.23, A.25, C.65, A.139, Q.145, D.163, H.164, W.190 Ligands: ARG-LEU-SER.1, CL.3, MPD.5, MPD.6 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.190 Hydrogen bonds: A:Q.19, A:Q.21, A:Q.21, A:Q.145, A:H.164, A:W.190 Water bridges: A:Q.21, A:G.23

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

CL.3: 8 residues within 4Å: Chain A: Q.19, G.23, S.24, A.25, H.164 Ligands: ARG-LEU-SER.1, ALA-LYS-PRO-NH2.2, MPD.5 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: F.69, M.70, A.71 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: R.8, N.197 Ligands: GOL.8 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: S.149, G.150, K.201 Ligand excluded by PLIP

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

MPD.4: 12 residues within 4Å: Chain A: W.26, G.67, G.68, F.69, M.70, A.136, L.162, D.163, H.164 Ligands: ARG-LEU-SER.1, ARG-LEU-SER.1, ARG-LEU-SER.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.68 MPD.5: 10 residues within 4Å: Chain A: A.139, G.140, Q.145, D.163, H.164, W.190 Ligands: ARG-LEU-SER.1, ALA-LYS-PRO-NH2.2, ALA-LYS-PRO-NH2.2, CL.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:H.164, A:W.190 Hydrogen bonds: A:D.163, A:H.164 Water bridges: A:D.163 MPD.6: 9 residues within 4Å: Chain A: N.18, Q.19, K.20, Q.21, Q.145, W.190 Ligands: ALA-LYS-PRO-NH2.2, ALA-LYS-PRO-NH2.2, ALA-LYS-PRO-NH2.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.145 Water bridges: A:N.18 MPD.14: 3 residues within 4Å: Chain A: K.99, Y.100, R.101 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.99

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 9 residues within 4Å: Chain A: R.8, Y.147, S.149, L.185, S.196, Y.199, V.200, K.201 Ligands: CL.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.8, A:R.8, A:Y.147 Water bridges: A:G.150 GOL.11: 6 residues within 4Å: Chain A: K.17, N.18, K.20, F.28, E.86, Y.91 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.18, A:K.20, A:E.50 Water bridges: A:V.16 GOL.12: 6 residues within 4Å: Chain A: V.77, K.78, G.81, Q.108, D.109, T.110 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.77, A:K.78, A:G.81 GOL.16: 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

2 x TFA: trifluoroacetic acid(Non-covalent)

TFA.13: 7 residues within 4Å: Chain A: E.120, K.121, M.124, K.182, W.184, K.204, D.205 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.205 Water bridges: A:K.182, A:K.182, A:K.204 Salt bridges: A:K.121, A:K.182, A:K.204 TFA.15: 4 residues within 4Å: Chain A: G.140, H.141, S.142, Q.145 4 PLIP interactions: 4 interactions with chain A Water bridges: A:H.141, A:Q.145 Halogen bonds: A:G.140, A:S.142

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
AA

Human cathepsin V

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