SMTL ID : 9b10.1 (1 other biounit)

Mycolicibacterium smegmatis ClpS with TyrArg dipeptide and Mg2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.28 Å

Oligo State

monomer

Ligands

1 x TYR: TYROSINE(Non-covalent)

TYR.1: 16 residues within 4Å: Chain A: V.11, W.12, D.13, D.14, P.15, N.17, L.18, M.19, V.22, M.41, V.44, H.45, L.72 Ligands: ARG.2, MG.3, MG.4 7 PLIP interactions: 2 Ligand-Ligand interactions, 5 interactions with chain A Water bridges: Y.1, R.2 Hydrophobic interactions: A:N.17, A:V.22, A:V.44 Hydrogen bonds: A:W.12, A:D.13

1 x ARG: ARGININE(Non-covalent)

ARG.2: 7 residues within 4Å: Chain A: P.15, V.16, N.17, L.18, M.19 Ligands: TYR.1, GOL.6 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:L.18 Hydrogen bonds: A:V.16, A:N.17, A:M.19 Water bridges: Y.1

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: V.11, W.12, D.14, L.72, W.73 Ligands: TYR.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:W.12, A:D.14, TYR.1 MG.4: 2 residues within 4Å: Chain A: H.45 Ligands: TYR.1 5 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: TYR.1, A:H.45, H2O.2, H2O.2, H2O.4 MG.5: 2 residues within 4Å: Chain A: D.79, R.80 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.79, H2O.1, H2O.3

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: V.16, N.17, L.18, Y.21 Ligands: ARG.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:V.16, A:N.17, A:L.18, R.2 GOL.7: 2 residues within 4Å: Chain A: Y.24, K.28 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Presloid, C.J. et al., ClpS Directs Degradation of N-Degron Substrates With Primary Destabilizing Residues in Mycolicibacterium smegmatis. Mol.Microbiol. (2024)

Release Date

2024-12-11

Peptides

ATP-dependent Clp protease adapter protein ClpS: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ATP-dependent Clp protease adapter protein ClpS

Related Entries With Identical Sequence