SMTL ID : 7qfh.1

Peptide AYFKKVL in complex with human cathepsin V C25A mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

homo-dimer

Ligands

2 x LYS- LYS- VAL- LEU: LYS-VAL-LEU-AMI(Non-covalent)

LYS-LYS-VAL-LEU.1: 21 residues within 4Å: Chain A: Q.19, G.23, S.24, A.25, W.26, Q.63, C.65, N.66, G.67, G.68, F.69, M.70, A.136, N.161, L.162, D.163, H.164, G.165 Ligands: MPD.3, MPD.9, NH2.21 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Q.63, A:F.69 Hydrogen bonds: A:Q.19, A:A.25, A:Q.63, A:N.66, A:G.68, A:G.68, A:D.163 Water bridges: A:R.72, A:D.163, A:G.165, A:G.165 LYS-LYS-VAL-LEU.2: 19 residues within 4Å: Chain B: Q.19, G.23, S.24, A.25, W.26, Q.63, C.65, N.66, G.67, G.68, F.69, M.70, A.136, L.162, D.163, H.164, G.165 Ligands: MPD.14, NH2.22 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.69 Hydrogen bonds: B:Q.19, B:A.25, B:N.66, B:G.68, B:G.68, B:D.163

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

MPD.3: 9 residues within 4Å: Chain A: A.139, G.140, Q.145, D.163, H.164, W.190 Ligands: LYS-LYS-VAL-LEU.1, MPD.6, NH2.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.139, A:D.163 MPD.5: 6 residues within 4Å: Chain A: K.17, N.18, F.28, E.50, E.86, Y.91 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:K.17, A:F.28, A:Y.91, A:Y.91 Hydrogen bonds: A:N.18, A:N.18 MPD.6: 8 residues within 4Å: Chain A: N.18, Q.19, K.20, Q.145, W.190, W.194 Ligands: MPD.3, MPD.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.145, A:W.190 Water bridges: A:N.18 MPD.8: 6 residues within 4Å: Chain A: Y.12, F.39, R.40, K.41, T.42, G.43 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.39 MPD.9: 8 residues within 4Å: Chain A: Q.19, K.20, Q.21, C.22, G.23, W.190 Ligands: LYS-LYS-VAL-LEU.1, MPD.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.190 Water bridges: A:Q.19 MPD.14: 9 residues within 4Å: Chain B: A.139, G.140, Q.145, D.163, H.164, W.190 Ligands: LYS-VAL-LEU.2, MPD.15, NH2.22 2 PLIP interactions: 2 interactions with chain B Water bridges: B:A.139, B:H.141 MPD.15: 8 residues within 4Å: Chain B: N.18, Q.19, K.20, Q.21, Q.145, W.190, W.194 Ligands: MPD.14 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Q.19, B:W.190 Hydrogen bonds: B:Q.21 MPD.16: 5 residues within 4Å: Chain B: P.59, Q.60, Y.76, E.79, N.80 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:N.80 Hydrogen bonds: B:Q.60 Water bridges: B:C.56 MPD.17: 9 residues within 4Å: Chain A: T.14, P.15, L.45, V.46, S.47 Chain B: K.10, G.11, F.39, G.43 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.14, A:P.15, B:F.39 Water bridges: A:L.45

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

CL.4: 3 residues within 4Å: Chain A: F.69, M.70, A.71 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: F.69, M.70, A.71 Ligand excluded by PLIP

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: F.112, T.113, V.114, N.220 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.112 GOL.10: 4 residues within 4Å: Chain A: Q.37, R.40, K.41, V.221 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.37, A:R.40 Water bridges: A:Q.37, A:V.221, A:V.221 GOL.11: 5 residues within 4Å: Chain A: M.38, T.42, K.44, V.46, V.106 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.42, A:T.42 Water bridges: A:V.106 GOL.18: 8 residues within 4Å: Chain B: D.84, S.88, Y.89, P.90, K.99, Y.100, R.101, N.104 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.84, B:R.101, B:N.104 GOL.19: 7 residues within 4Å: Chain B: T.113, V.115, K.125, A.126, T.129, V.130, Y.218 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.129 GOL.20: 5 residues within 4Å: Chain B: R.8, L.185, S.196, Y.199, K.201 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.8, B:R.8, B:S.196 Water bridges: B:Y.183, B:K.201

1 x TFA: trifluoroacetic acid(Non-covalent)

TFA.12: 8 residues within 4Å: Chain A: R.8, L.185, S.196, N.197, Y.199, K.201 Chain B: P.15, P.192 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.196, A:N.197 Salt bridges: A:R.8

2 x NH2: AMINO GROUP(Non-functional Binders)

NH2.21: 8 residues within 4Å: Chain A: Q.19, A.25, D.163, H.164, G.165 Ligands: LYS-LYS-VAL-LEU.1, LYS-LYS-VAL-LEU.1, MPD.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.163 Water bridges: A:Q.19, A:G.165 NH2.22: 8 residues within 4Å: Chain B: Q.19, A.25, D.163, H.164, G.165 Ligands: LYS-VAL-LEU.2, LYS-VAL-LEU.2, MPD.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.163 Water bridges: B:Q.19

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AA

B
BA

Cathepsin L2

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