SMTL ID : 6cn8.1

High-resolution structure of ClpC1-NTD binding to Rufomycin-I

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x F7P- MLE- NIY- ALA- F7S- LEU- F7V: Rufomycin I(Non-covalent)

F7P-MLE-NIY-ALA-F7S-LEU-F7V.1: 14 residues within 4Å: Chain A: M.1, F.2, R.10, V.13, Q.17, I.28, H.77, I.78, P.79, F.80, K.85, L.88, E.89 Ligands: CL.8 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.2, A:F.2, A:R.10, A:V.13, A:H.77, A:K.85, A:L.88 Hydrogen bonds: A:F.80, A:K.85 pi-Stacking: A:F.2

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 8 residues within 4Å: Chain A: G.29, T.30, E.31, T.81, R.83, A.84, G.118, V.119 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.30, A:A.84, A:V.119 Water bridges: A:R.83, A:R.83 Salt bridges: A:R.83

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

CL.3: 6 residues within 4Å: Chain A: T.30, G.118, V.119, A.120, A.121 Ligands: NA.4 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: T.6, R.8, G.104, T.105 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: S.55, L.56, E.57 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: M.1, F.2, E.3 Ligands: F7P-MLE-NIY-ALA-F7S-LEU-F7V.1 Ligand excluded by PLIP

4 x NA: SODIUM ION(Non-functional Binders)

NA.4: 6 residues within 4Å: Chain A: T.30, V.87, L.112, E.115, G.116 Ligands: CL.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.115, A:E.115, A:G.116 NA.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.9: 1 residues within 4Å: Ligands: NA.10 No protein-ligand interaction detected (PLIP) NA.10: 1 residues within 4Å: Ligands: NA.9 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wolf, N.M. et al., High-Resolution Structure of ClpC1-Rufomycin and Ligand Binding Studies Provide a Framework to Design and Optimize Anti-Tuberculosis Leads. Acs Infect Dis. (2019)

Release Date

2019-06-05

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

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