SMTL ID : 4ly6.4 (3 other biounits)

Nucleotide-induced asymmetry within ATPase activator ring drives s54-RNAP interaction and ATP hydrolysis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.60 Å

Oligo State

homo-hexamer

Ligands

5 x 08T: [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium(Non-covalent)(Covalent)

08T.1: 23 residues within 4Å: Chain A: Y.20, V.21, F.22, E.49, S.50, G.51, V.52, G.53, K.54, E.55, V.56, D.119, E.120, N.161, L.201, H.204, F.205, V.237, R.238, K.241 Chain B: D.176, R.180 Ligands: MG.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:V.21, A:V.21, A:G.51, A:V.52, A:G.53, A:K.54, A:E.55, A:V.56, A:K.241 Salt bridges: A:K.54, A:R.238, A:R.238 08T.3: 26 residues within 4Å: Chain B: Y.20, V.21, F.22, M.27, E.49, S.50, G.51, V.52, G.53, K.54, E.55, V.56, D.119, E.120, R.194, L.201, H.204, F.205, V.237, R.238, K.241 Chain C: L.133, E.137, D.176, R.180 Ligands: MG.4 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.50, B:G.51, B:V.52, B:G.53, B:K.54, B:E.55, B:V.56, B:R.194 Salt bridges: B:K.54, B:R.238, B:R.238 08T.5: 22 residues within 4Å: Chain C: Y.20, V.21, F.22, M.27, S.50, G.51, V.52, G.53, K.54, E.55, V.56, N.161, R.194, L.201, F.205, V.237, R.238, K.241 Chain D: E.137, D.176, R.180 Ligands: MG.6 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:V.21, C:G.51, C:V.52, C:G.53, C:G.53, C:K.54, C:E.55, C:V.56, C:R.194 Salt bridges: C:K.54, C:R.238 08T.7: 24 residues within 4Å: Chain D: E.19, Y.20, V.21, M.27, E.49, S.50, G.51, V.52, G.53, K.54, E.55, V.56, D.119, E.120, N.161, R.194, L.201, F.205, V.237, R.238, K.241 Chain E: D.176, R.180 Ligands: MG.8 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:V.21, D:S.50, D:G.51, D:V.52, D:G.53, D:K.54, D:E.55, D:E.55, D:V.56 Salt bridges: D:K.54, D:R.238, D:R.238 08T.9: 25 residues within 4Å: Chain E: E.19, Y.20, V.21, F.22, M.27, S.50, G.51, V.52, G.53, K.54, E.55, V.56, D.119, E.120, N.161, R.194, L.201, F.205, V.237, R.238, K.241 Chain F: L.133, D.176, R.180 Ligands: MG.10 14 PLIP interactions: 13 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:V.21, E:S.50, E:G.51, E:V.52, E:G.53, E:K.54, E:E.55, E:E.55, E:V.56, E:R.194, F:R.180 Salt bridges: E:K.54, E:R.238, E:R.238

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: E.55, D.119 Chain B: R.180 Ligands: 08T.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.119, A:D.119 MG.4: 5 residues within 4Å: Chain B: D.119, E.120, R.238 Chain C: R.180 Ligands: 08T.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.119 MG.6: 6 residues within 4Å: Chain C: K.54, D.119, N.161, R.238 Chain D: R.180 Ligands: 08T.5 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain D: D.119, E.120 Chain E: R.180 Ligands: 08T.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.119 MG.10: 4 residues within 4Å: Chain E: K.54, D.119, E.120 Ligands: 08T.9 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.119, E:D.119

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.11: 17 residues within 4Å: Chain F: E.19, Y.20, V.21, S.50, G.51, V.52, G.53, K.54, E.55, V.56, D.119, E.120, N.161, L.201, F.205, V.237, R.238 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:S.50, F:S.50, F:G.51, F:V.52, F:G.53, F:K.54, F:E.55, F:E.120, F:E.120 Salt bridges: F:K.54, F:K.54, F:R.238, F:R.238 pi-Stacking: F:F.205

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sysoeva, T.A. et al., Nucleotide-induced asymmetry within ATPase activator ring drives sigma 54-RNAP interaction and ATP hydrolysis. Genes Dev. (2013)

Release Date

2013-12-04

Peptides

Transcriptional regulator (NtrC family): ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
S

B
T

C
U

D
V

E
W

F
X

Transcriptional regulator (NtrC family)

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