SMTL ID : 9b10.2 (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

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 5 residues within 4Å: Chain A: S.20, T.23, E.34, T.38, M.41 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.34 EDO.2: 4 residues within 4Å: Chain A: H.45, N.46, E.47, G.48 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.46 EDO.9: 6 residues within 4Å: Chain A: I.10, W.12, T.75, M.76, Q.77 Ligands: PGE.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.76, A:Q.77 Water bridges: A:M.76

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 6 residues within 4Å: Chain A: I.10, W.12, K.49, V.51, Q.77 Ligands: EDO.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.49

1 x TYR: TYROSINE(Non-covalent)

TYR.4: 17 residues within 4Å: Chain A: V.11, W.12, D.13, D.14, P.15, N.17, L.18, M.19, V.22, F.26, M.41, V.44, H.45, L.72 Ligands: ARG.5, MG.7, MG.8 6 PLIP interactions: 6 interactions with chain A, Hydrophobic interactions: A:N.17, A:V.22, A:V.22, A:V.44 Hydrogen bonds: A:D.14, A:H.45

1 x ARG: ARGININE(Non-covalent)

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

1 x NI: NICKEL (II) ION(Non-covalent)

NI.6: 2 residues within 4Å: Chain A: E.58, E.61 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.58, A:E.61, H2O.1, H2O.1, H2O.3

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 6 residues within 4Å: Chain A: V.11, W.12, D.14, L.72, W.73 Ligands: TYR.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:W.12, A:D.14, TYR.4 MG.8: 2 residues within 4Å: Chain A: H.45 Ligands: TYR.4 5 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions, 3 Ligand-Water interactions Metal complexes: A:H.45, TYR.4, H2O.1, H2O.4, H2O.5

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
B

ATP-dependent Clp protease adapter protein ClpS

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