SMTL ID : 9guj.1

Crystal structure of transcription factor NtcA from Synechococcus elongatus in complex with its transcriptional co- activator PipX and its target DNA (Crystal II)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.30 Å

Oligo State

hetero-4-3-mer

Ligands

4 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.1: 10 residues within 4Å: Chain A: F.34, L.53, F.74, G.75, V.76, L.77, R.87, Y.89, R.128 Chain B: E.133 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.89 Hydrogen bonds: A:G.75, A:V.76, A:L.77, B:E.133 Salt bridges: A:R.87, A:R.128 AKG.2: 10 residues within 4Å: Chain A: E.133 Chain B: F.34, L.53, F.74, G.75, V.76, L.77, R.87, Y.89, R.128 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.34, B:L.53, B:Y.89 Hydrogen bonds: B:G.75, B:V.76, B:L.77 Salt bridges: B:R.87, B:R.128 AKG.3: 10 residues within 4Å: Chain G: F.34, L.53, F.74, G.75, V.76, L.77, R.87, Y.89, R.128 Chain H: E.133 8 PLIP interactions: 7 interactions with chain G, 1 interactions with chain H Hydrophobic interactions: G:F.34, G:Y.89 Hydrogen bonds: G:G.75, G:V.76, G:L.77, H:E.133 Salt bridges: G:R.87, G:R.128 AKG.4: 11 residues within 4Å: Chain G: I.129, L.130, E.133 Chain H: F.34, L.53, F.74, G.75, V.76, L.77, Y.89, R.128 7 PLIP interactions: 5 interactions with chain H, 2 interactions with chain G Hydrophobic interactions: H:Y.89, G:L.130 Hydrogen bonds: H:G.75, H:V.76, H:L.77, G:E.133 Salt bridges: H:R.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Forcada-Nadal, A. et al., Structures of the cyanobacterial nitrogen regulators NtcA and PipX complexed to DNA shed light on DNA binding by NtcA and implicate PipX in the recruitment of RNA polymerase. Nucleic Acids Res. (2025)

Release Date

2025-03-12

Peptides

Global nitrogen regulator: ABGH
PipX: EFK

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
F

G
A

H
B

E
J

F
H

K
K

Global nitrogen regulator

PipX

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