SMTL ID : 6qjx.1

TetR(D) T103A mutant in complex with minocycline and magnesium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x MIY: (4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE(Non-covalent)

MIY.1: 16 residues within 4Å: Chain A: L.59, H.63, S.66, N.81, F.85, H.99, T.111, Q.115, L.130, I.133, S.134, S.137, H.138 Chain B: E.146, M.176 Ligands: MG.2 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.133 Hydrogen bonds: A:H.63, A:S.66, A:N.81, A:Q.115, A:S.137, B:E.146 Water bridges: A:Q.108 MIY.7: 16 residues within 4Å: Chain A: E.146, M.176 Chain B: L.59, H.63, S.66, N.81, F.85, H.99, T.111, Q.115, L.130, I.133, S.134, S.137, H.138 Ligands: MG.8 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.133 Hydrogen bonds: B:H.63, B:S.66, B:N.81, B:Q.115, B:S.137, A:E.146 Water bridges: B:Q.108

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: H.99 Ligands: MIY.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.99, H2O.1, H2O.1, H2O.1 MG.8: 2 residues within 4Å: Chain B: H.99 Ligands: MIY.7 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.99, H2O.2, H2O.2, H2O.3

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

CL.3: 2 residues within 4Å: Chain A: R.2, L.3 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: T.25, T.26 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: N.4, R.5, E.6 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: S.1, R.2 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain B: R.2, L.3 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain B: T.25, T.26 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: N.4, R.5, E.6 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: S.1, R.2 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Palm, G.J. et al., Thermodynamics, cooperativity and stability of the tetracycline repressor (TetR) upon tetracycline binding. Biochim Biophys Acta Proteins Proteom (2020)

Release Date

2019-08-21

Peptides

Tetracycline repressor protein class D: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Tetracycline repressor protein class D

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