SMTL ID : 2be5.1 (1 other biounit)

Crystal structure of the T. Thermophilus RNA polymerase holoenzyme in complex with inhibitor tagetitoxin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-2-1-1-1-1-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain C: E.685, R.879 Chain D: D.739, R.1029 Ligands: TGT.5 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:D.739, C:E.685, H2O.77 MG.4: 3 residues within 4Å: Chain D: D.739, D.741, D.743 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.739, D:D.741, D:D.741, D:D.743, D:D.743

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain D: C.58, C.60, C.73, C.76 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.58, D:C.60, D:C.73, D:C.76 ZN.3: 5 residues within 4Å: Chain D: C.1112, R.1189, C.1194, C.1201, C.1204 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.1112, D:C.1194, D:C.1201, D:C.1204

1 x TGT: TAGETITOXIN(Non-covalent)

TGT.5: 11 residues within 4Å: Chain C: R.557, S.878, R.879 Chain D: N.737, D.739, R.783, R.1029, G.1030, N.1031, Q.1034 Ligands: MG.1 16 PLIP interactions: 9 interactions with chain D, 7 interactions with chain C Hydrogen bonds: D:N.737, D:R.783, D:G.1030, D:N.1031, D:Q.1034, C:S.878, C:S.878 Water bridges: D:R.1029, D:N.1031, C:R.557, C:R.557, C:R.879 Salt bridges: D:R.783, D:R.1029, C:R.557, C:R.879

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vassylyev, D.G. et al., Structural basis for transcription inhibition by tagetitoxin. Nat.Struct.Mol.Biol. (2005)

Release Date

2005-11-08

Peptides

DNA-directed RNA polymerase alpha chain: AB
DNA-directed RNA polymerase beta chain: C
DNA-directed RNA polymerase beta' chain: D
RNA polymerase omega chain: E
RNA polymerase sigma factor rpoD: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

DNA-directed RNA polymerase alpha chain

DNA-directed RNA polymerase beta chain

DNA-directed RNA polymerase beta' chain

RNA polymerase omega chain

RNA polymerase sigma factor rpoD

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