SMTL ID : 2o7o.1

Crystal structure analysis of TetR(D) complex with doxycycline

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: H.99 Ligands: DXT.5 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.99, H2O.1, H2O.1, H2O.1 MG.6: 2 residues within 4Å: Chain B: H.99 Ligands: DXT.10 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.99, H2O.4, H2O.4, H2O.5

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: R.61, H.62, R.91, Y.92 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.61, A:Y.92, A:Y.92 Salt bridges: A:H.62, A:R.91 SO4.7: 4 residues within 4Å: Chain B: R.61, H.62, R.91, Y.92 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.61, B:Y.92, B:Y.92 Salt bridges: B:H.62, B:R.91

4 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: S.73, S.76 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain B: R.2, L.3 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain B: S.73, S.76 Ligand excluded by PLIP

2 x DXT: (4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12,12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE(Non-covalent)

DXT.5: 18 residues within 4Å: Chain A: L.59, H.63, S.66, N.81, F.85, H.99, T.102, R.103, P.104, T.111, V.112, Q.115, I.133, S.137 Chain B: L.169, L.173, M.176 Ligands: MG.1 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.104, A:V.112, B:L.169, B:L.173 Hydrogen bonds: A:H.63, A:N.81, A:R.103, A:Q.115, A:Q.115 Water bridges: A:Q.108, A:S.137 DXT.10: 18 residues within 4Å: Chain A: L.169, L.173, M.176 Chain B: L.59, H.63, S.66, N.81, F.85, H.99, T.102, R.103, P.104, T.111, V.112, Q.115, I.133, S.137 Ligands: MG.6 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.104, B:V.112, A:L.169, A:L.173 Hydrogen bonds: B:H.63, B:N.81, B:R.103, B:Q.115, B:Q.115 Water bridges: B:Q.108, B:S.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aleksandrov, A. et al., Protonation Patterns in Tetracycline:Tet Repressor Recognition: Simulations and Experiments. Chembiochem (2007)

Release Date

2007-05-15

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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