SMTL ID : 4mq9.1

Crystal structure of Thermus thermophilus RNA polymerase holoenzyme in complex with GE23077

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.35 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, A.1085, T.1088 Ligands: MB8.5 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:E.445, C:E.445, C:E.445, C:E.445, C:G.446, C:R.557, C:N.563, C:Q.567, C:K.838, C:K.846 Salt bridges: C:R.405

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: 6 residues within 4Å: Chain D: C.1112, R.1189, C.1194, Q.1195, 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 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

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

MB8.5: 4 residues within 4Å: Chain C: R.409, 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
RNA polymerase sigma factor: 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

RNA polymerase sigma factor

Related Entries With Identical Sequence