SMTL ID : 8b9u.1

Structure of ClpC1 NTD from Mycobacterium tuberculosis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

1 x MLE- VAL- MAA- E9M- GLY: (MLE)V(MAA)(E9M)G(Non-covalent)

MLE-VAL-MAA-E9M-GLY.1: 15 residues within 4Å: Chain A: E.3, F.5, L.88, E.89, L.92 Chain B: F.2, R.10, R.11, V.13, V.14, Q.17, I.28, I.78, F.80 Ligands: FMT.6 15 PLIP interactions: 10 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:F.2, B:R.10, B:R.10, B:V.13, B:V.14, A:F.5 Hydrogen bonds: B:R.11, B:Q.17, B:Q.17, A:E.3, A:E.89 Water bridges: B:R.11, A:K.85, A:E.89 pi-Stacking: B:F.2

7 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 8 residues within 4Å: Chain A: G.29, T.30, E.31, T.81, R.83, A.84, G.118, V.119 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.30, A:T.81, A:A.84, A:V.119 FMT.3: 5 residues within 4Å: Chain A: Q.17, E.18, R.21 Chain B: A.73, P.74 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.17, A:R.21 Water bridges: A:E.18 FMT.4: 3 residues within 4Å: Chain A: R.11, V.14 Chain B: S.75 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.75, A:R.11 FMT.5: 7 residues within 4Å: Chain B: G.29, T.30, E.31, T.81, R.83, G.118, V.119 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.30, B:T.81, B:V.119 FMT.6: 4 residues within 4Å: Chain A: F.80 Chain B: Q.17, R.21 Ligands: MLE-VAL-MAA-E9M-GLY.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.21 Water bridges: B:Q.17, B:I.78 FMT.7: 4 residues within 4Å: Chain B: G.43, V.44, T.105, E.106 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.44, B:T.105, B:E.106 Water bridges: B:E.42 FMT.8: 3 residues within 4Å: Chain B: Y.27, P.79, F.80 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hoi, D.M. et al., Clp-targeting BacPROTACs impair mycobacterial proteostasis and survival. Cell (2023)

Release Date

2023-07-05

Peptides

ATP-dependent Clp protease ATP-binding subunit ClpC1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ATP-dependent Clp protease ATP-binding subunit ClpC1