SMTL ID : 3n4m.1

E. coli RNA polymerase alpha subunit C-terminal domain in complex with CAP and DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.99 Å

Oligo State

hetero-2-4-mer

Ligands

4 x CMP: ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE(Non-covalent)(Non-functional Binders)

CMP.1: 18 residues within 4Å: Chain A: I.30, V.49, L.61, S.62, I.70, G.71, E.72, L.73, G.74, R.82, S.83, A.84, V.86, Y.99, R.123, T.127 Chain F: L.124, S.128 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain F Hydrogen bonds: A:G.71, A:E.72, A:E.72, A:L.73, A:G.74, A:S.83, A:Y.99, A:R.123, A:T.127, F:S.128, F:S.128 Salt bridges: A:R.82 CMP.4: 4 residues within 4Å: Chain D: T.17, G.18 Chain E: C.7, A.8 No protein-ligand interaction detected (PLIP) CMP.5: 18 residues within 4Å: Chain A: L.124, S.128 Chain F: I.30, V.49, L.61, S.62, I.70, G.71, E.72, L.73, G.74, R.82, S.83, A.84, V.86, Y.99, R.123, T.127 11 PLIP interactions: 9 interactions with chain F, 2 interactions with chain A Hydrogen bonds: F:G.71, F:E.72, F:E.72, F:L.73, F:G.74, F:S.83, F:Y.99, F:R.123, A:S.128, A:S.128 Salt bridges: F:R.82 CMP.8: 4 residues within 4Å: Chain I: T.17, G.18 Chain J: C.7, A.8 No protein-ligand interaction detected (PLIP)

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 4 residues within 4Å: Chain A: T.10, W.13, V.108, N.109 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.109 PEG.3: 2 residues within 4Å: Chain A: D.161, Y.206 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.161 PEG.6: 4 residues within 4Å: Chain F: T.10, W.13, V.108, N.109 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.109 PEG.7: 2 residues within 4Å: Chain F: D.161, Y.206 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lara-Gonzalez, S. et al., The RNA Polymerase alpha Subunit Recognizes the DNA Shape of the Upstream Promoter Element. Biochemistry (2020)

Release Date

2011-05-25

Peptides

Catabolite gene activator: AF
DNA-directed RNA polymerase subunit alpha: BCGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
A

B
B

C
C

G
B

H
C

Catabolite gene activator

DNA-directed RNA polymerase subunit alpha

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