SMTL ID : 4oio.1

Crystal structure of Thermus thermophilus pre-insertion substrate complex for de novo transcription initiation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

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

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain D: C.1112, R.1189, C.1194, Q.1195, T.1196, 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 ZN.2: 5 residues within 4Å: Chain D: C.58, C.60, K.62, 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

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain D: D.739, D.741, D.743 Ligands: ATP.5 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.739, D:D.741, D:D.741, D:D.743 MG.4: 4 residues within 4Å: Chain C: E.685, R.879 Chain D: D.739 Ligands: 2TM.6 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.739

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.5: 14 residues within 4Å: Chain C: Q.567, K.838, K.846, H.999 Chain D: R.704, A.705, D.739, D.741, G.742, D.743 Chain G: T.15, C.16 Ligands: MG.3, 2TM.6 11 PLIP interactions: 4 interactions with chain D, 7 interactions with chain C Hydrogen bonds: D:R.704, C:Q.567, C:Q.567 Water bridges: D:D.739, D:Q.744, D:Q.744 Salt bridges: C:K.838, C:K.838, C:K.846, C:H.999, C:H.999

1 x 2TM: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine(Non-covalent)

2TM.6: 12 residues within 4Å: Chain C: E.445, S.878, R.879 Chain D: R.704, P.706, N.737, D.739, R.1029 Chain G: G.14, T.15 Ligands: MG.4, ATP.5 11 PLIP interactions: 6 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:R.704, D:R.704, D:N.737, C:E.445, C:S.878, C:S.878 Water bridges: D:R.783, D:R.783, C:R.879 Salt bridges: D:R.1029, C:R.879

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Y. et al., GE23077 binds to the RNA polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides. Elife (2014)

Release Date

2014-05-07

Peptides

DNA-directed RNA polymerase subunit alpha: AB
DNA-directed RNA polymerase subunit beta: C
DNA-directed RNA polymerase subunit beta': D
DNA-directed RNA polymerase subunit omega: E
DNA directed RNA polymerase sigma factor A: 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 subunit alpha

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase subunit beta'

DNA-directed RNA polymerase subunit omega

DNA directed RNA polymerase sigma factor A

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