SMTL ID : 4q4z.1

Thermus thermophilus RNA polymerase de novo transcription initiation complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

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

Ligands

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

ATP.1: 13 residues within 4Å: Chain C: Q.567, K.838, K.846, H.999, K.1004 Chain D: R.704, D.741, G.742, D.743 Chain G: T.15, G.16 Ligands: MG.4, 2TM.7 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:Q.567, D:R.704, D:R.704 Salt bridges: C:K.838, C:K.838, C:H.999, C:H.999, C:K.1004 Water bridges: D:D.741

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 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.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

3 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain D: D.739, D.741, D.743 Ligands: ATP.1 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.739, D:D.741, D:D.743, H2O.2, H2O.2 MG.5: 2 residues within 4Å: Chain D: D.739 Ligands: 2TM.7 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain B: D.168 Chain D: K.840, Y.841 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:K.840, H2O.1

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

2TM.7: 12 residues within 4Å: Chain C: R.557, R.879 Chain D: R.704, P.706, N.737, R.1029, Q.1235, M.1238, T.1240 Chain G: G.14 Ligands: ATP.1, MG.5 9 PLIP interactions: 2 interactions with chain C, 7 interactions with chain D Hydrogen bonds: C:R.557, D:R.704, D:R.704, D:N.737, D:R.1029, D:R.1029, D:Q.1235, D:T.1240 Salt bridges: C:R.879

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

2014-07-30

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

Related Entries With Identical Sequence