SMTL ID : 4q5s.1

Thermus thermophilus RNA polymerase initially transcribing complex containing 6-mer RNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

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

Ligands

1 x C- U- C- A- C: RNA (5'-R(P*CP*UP*CP*AP*C)-3')(Non-covalent)

C-U-C-A-C.1: 28 residues within 4Å: Chain C: R.409, L.413, R.420, P.444, E.445, N.448, I.452, Q.567, K.838, K.846, H.999 Chain D: R.704, P.706, N.737, D.739, D.741, G.742, D.743, Q.1235, M.1238 Chain G: G.10, T.11, G.12, A.13, G.14, T.15 Ligands: MG.2, ATP.5 Protein-ligand interaction information (PLIP) not available

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain D: D.739, D.741, D.743 Ligands: C-U-C-A-C.1, C-U-C-A-C.1 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.739, D:D.741, D:D.743, D:D.743

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain D: C.58, A.59, 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.4: 6 residues within 4Å: Chain D: C.1112, T.1114, 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 ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.5: 7 residues within 4Å: Chain C: Q.390, Q.393, R.420 Chain G: G.14, T.15, G.16 Ligands: C-U-C-A-C.1 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.393

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Basu, R.S. et al., Structural basis of transcription initiation by bacterial RNA polymerase holoenzyme. J.Biol.Chem. (2014)

Release Date

2014-07-09

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 SigA: 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 SigA

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