SMTL ID : 6rxb.1 (1 other biounit)

Crystal structure of TetR-Q116A from Acinetobacter baumannii AYE in complex with minocycline

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 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.60, H.64, S.67, N.82, F.86, H.100, T.103, R.104, P.105, I.117, V.131, L.134, R.135, V.137, S.138 Ligands: MG.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:P.105 Hydrogen bonds: A:H.64, A:N.82, A:H.100, A:T.103, A:R.104 Water bridges: A:A.83, A:R.135, A:S.138, A:S.138 MIY.3: 16 residues within 4Å: Chain A: F.176 Chain B: L.60, H.64, S.67, N.82, F.86, H.100, T.103, R.104, P.105, N.109, A.113, V.131, L.134, S.138 Ligands: MG.4 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:P.105 Hydrogen bonds: B:H.64, B:N.82, B:H.100, B:T.103, B:R.104, B:N.109 Water bridges: B:S.138, B:S.138

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: H.100, T.103 Chain B: E.147 Ligands: MIY.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.100, H2O.1, H2O.2, H2O.2 MG.4: 4 residues within 4Å: Chain A: E.147 Chain B: H.100, T.103 Ligands: MIY.3 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.100, H2O.1, H2O.1, H2O.3

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

EDO.5: 3 residues within 4Å: Chain B: D.95, R.98, A.150 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.98 Water bridges: B:D.95

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

CL.6: 2 residues within 4Å: Chain B: C.126, R.129 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sumyk, M. et al., Binding of Tetracyclines to Acinetobacter baumannii TetR Involves Two Arginines as Specificity Determinants. Front Microbiol (2021)

Release Date

2020-07-15

Peptides

Tetracycline repressor protein class G: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Tetracycline repressor protein class G

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