SMTL ID : 1smy.2 (1 other biounit)

Structural basis for transcription regulation by alarmone ppGpp

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

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

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain C: E.685 Chain D: D.739, R.1029 Ligands: G4P.7 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:D.739, C:E.685, H2O.118, H2O.118 MG.4: 3 residues within 4Å: Chain D: D.739, D.741, D.743 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.739, D:D.741, D:D.743, H2O.132 MG.5: 2 residues within 4Å: Chain D: R.783 Ligands: G4P.7 No protein-ligand interaction detected (PLIP)

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: 5 residues within 4Å: Chain D: C.1112, R.1189, 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

2 x G4P: GUANOSINE-5',3'-TETRAPHOSPHATE(Non-functional Binders)(Non-covalent)

G4P.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) G4P.7: 15 residues within 4Å: Chain C: E.685, S.878, R.879 Chain D: E.734, N.737, R.783, K.908, G.1027, A.1028, R.1029, E.1231, T.1234, Q.1235 Ligands: MG.1, MG.5 18 PLIP interactions: 14 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:E.734, D:N.737, D:T.1234, D:Q.1235, C:E.685, C:S.878, C:S.878 Water bridges: D:K.908, D:K.908, D:Q.1034, D:Q.1235 Salt bridges: D:R.783, D:K.908, D:K.908, D:R.1029, D:R.1029, D:E.1231, C:R.879

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Artsimovitch, I. et al., Structural basis for transcription regulation by alarmone ppGpp. Cell(Cambridge,Mass.) (2004)

Release Date

2004-05-18

Peptides

DNA-directed RNA polymerase alpha chain: AB
DNA-directed RNA polymerase beta chain: C
DNA-directed RNA polymerase beta' chain: D
RNA POLYMERASE OMEGA SUBUNIT: E
principal sigma factor: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

B
L

C
M

D
N

E
O

F
P

DNA-directed RNA polymerase alpha chain

DNA-directed RNA polymerase beta chain

DNA-directed RNA polymerase beta' chain

RNA POLYMERASE OMEGA SUBUNIT

principal sigma factor

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