SMTL ID : 4oin.1

Crystal structure of Thermus thermophilus transcription initiation complex soaked with GE23077

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

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

Ligands

1 x 2RA- DSN- DVA- R2T- 2TL- 0QZ- FGL: GE23077(Non-covalent)

2RA-DSN-DVA-R2T-2TL-0QZ-FGL.1: 15 residues within 4Å: Chain C: P.444, E.445, G.446, R.557, L.559, M.560, N.563, M.564, Q.567, K.838, K.846 Chain D: D.741, T.1084 Chain G: G.17 Ligands: MB8.9 18 PLIP interactions: 2 interactions with chain D, 16 interactions with chain C Hydrophobic interactions: D:T.1084 Water bridges: D:D.741, C:R.405, C:R.405, C:E.445, C:R.557, C:R.879 Hydrogen bonds: C:E.445, C:E.445, C:E.445, C:E.445, C:G.446, C:A.447, C:R.557, C:N.563, C:Q.567, C:K.838, C:K.846

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain B: D.183, D.191, D.193 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.191, B:D.193 MG.5: 3 residues within 4Å: Chain D: D.739, D.741, D.743 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.739, D:D.741, D:D.743, H2O.11, H2O.11, H2O.11 MG.6: 3 residues within 4Å: Chain B: D.168 Chain D: K.840, Y.841 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.2, H2O.2, H2O.2, H2O.11, H2O.11 MG.7: 3 residues within 4Å: Chain D: W.897, E.898, I.900 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain F: A.312, G.316, W.319 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:A.312, F:G.316, F:W.319, H2O.22

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain D: C.1112, 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.4: 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

1 x MB8: (2Z)-2-methylbut-2-enoic acid(Non-covalent)

MB8.9: 3 residues within 4Å: Chain C: P.444, N.448 Ligands: 2RA-DSN-DVA-R2T-2TL-0QZ-FGL.1 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.448

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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