SMTL ID : 9din.1

Structure of ClpC1 N-terminal Domain complexed with semi-synthetic Rufomycin analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

monomer

Ligands

1 x 01- MLE- NIY- ALA- 02- LEU- NLE: Rufomycin analog(Non-covalent)

01-MLE-NIY-ALA-02-LEU-NLE.1: 14 residues within 4Å: Chain A: A.1, F.2, R.10, V.13, V.14, Q.17, I.28, H.77, I.78, P.79, F.80, K.85, L.88, E.89 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.1, A:F.2, A:R.10, A:H.77, A:K.85, A:K.85, A:L.88, A:L.88 Hydrogen bonds: A:F.80 pi-Stacking: A:F.2

1 x ACY: ACETIC ACID(Non-functional Binders)

ACY.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 Hydrophobic interactions: A:V.119 Hydrogen bonds: A:T.30, A:A.84, A:V.119

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: I.66, I.67, V.119, Q.122 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.122, A:Q.122

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

CL.4: 4 residues within 4Å: Chain A: T.6, R.8, G.104, T.105 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, B. et al., Structure-Based Analysis of Semisynthetic Anti-TB Rufomycin Analogues. J.Nat.Prod. (2025)

Release Date

2025-04-16

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ATP-dependent Clp protease ATP-binding subunit ClpC1