SMTL ID : 9bdw.1

NF-kappaB RelA homo-dimer bound to GC-centric kappaB DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-dimer

Ligands

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 7 residues within 4Å: Chain A: Y.19, H.71, C.103, L.137, N.138, D.168 Chain B: T.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.19, A:D.168, A:D.168 Salt bridges: A:H.71 SO4.2: 7 residues within 4Å: Chain A: T.61, K.62, D.63, R.67, D.134, Y.135, D.136 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.61, A:K.62, A:D.63, A:D.136 Water bridges: A:D.63, A:R.67, A:D.136 Salt bridges: A:R.67 SO4.3: 8 residues within 4Å: Chain A: S.28, I.29, H.41, P.42, F.96, Q.97, N.98, L.99 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:I.29, A:I.29, A:Q.97, A:L.99 Water bridges: A:Q.97 Salt bridges: A:H.41 SO4.4: 7 residues within 4Å: Chain A: K.11, Q.12, R.13, G.14, M.15, I.166, F.167 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:M.15, A:F.167, A:F.167 Water bridges: A:R.13, A:G.14 SO4.6: 7 residues within 4Å: Chain D: T.61, K.62, D.63, R.67, D.134, Y.135, D.136 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:K.62, D:D.63, D:D.136 Water bridges: D:H.69, D:D.136 Salt bridges: D:R.67

1 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.5: 3 residues within 4Å: Chain B: A.1 Chain C: T.19 Chain D: Y.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, T. et al., Transient interactions modulate the affinity of NF-kappa B transcription factors for DNA. Proc.Natl.Acad.Sci.USA (2024)

Release Date

2024-04-24

Peptides

Transcription factor p65: AD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

D
A

Transcription factor p65

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