SMTL ID : 4oiq.1

Crystal structure of Thermus thermophilus transcription initiation complex soaked with GE23077 and rifampicin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.62 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: 14 residues within 4Å: Chain C: P.444, E.445, G.446, R.557, L.559, M.560, N.563, Q.567, K.838, K.846 Chain D: D.741, T.1084 Chain G: C.16 Ligands: MB8.8 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:E.445, C:E.445, C:E.445, C:E.445, C:E.445, C:E.445, C:G.446, C:R.557, C:R.557, C:N.563, C:N.563, C:Q.567, C:K.838, C:K.846 Hydrophobic interactions: D:T.1084

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain D: C.1112, 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 ZN.3: 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

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain D: D.739, D.741, D.743 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.739, D:D.741, D:D.743, H2O.1, H2O.1 MG.5: 4 residues within 4Å: Chain B: E.154, D.168 Chain D: K.840, Y.841 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:K.840 MG.6: 3 residues within 4Å: Chain D: W.897, E.898, I.900 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:W.897 MG.7: 5 residues within 4Å: Chain F: A.312, E.313, G.316, P.317, W.319 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:A.312, F:G.316

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

MB8.8: 4 residues within 4Å: Chain G: C.16, G.17 Ligands: 2RA-DSN-DVA-R2T-2TL-0QZ-FGL.1, 2RA-DSN-DVA-R2T-2TL-0QZ-FGL.1 No protein-ligand interaction detected (PLIP)

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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