SMTL ID : 8qu2.1

NF-YB/C Heterodimer in Complex with a 16-mer NF-YA-derived Peptide Stabilized with C8-Hydrocarbon Linker

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.1: 5 residues within 4Å: Chain A: X.1, L.4, I.7 Chain C: D.88, I.91 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.88, C:D.88

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 2 residues within 4Å: Chain A: K.9, Q.12 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.12 Water bridges: A:R.6, B:S.51 FMT.3: 1 residues within 4Å: Chain B: P.25 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.26

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 3 residues within 4Å: Chain C: P.20, R.23 Ligands: EDO.5 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.23 EDO.5: 2 residues within 4Å: Chain C: R.23 Ligands: EDO.4 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Durukan, C. et al., Binding Dynamics of a Stapled Peptide Targeting the Transcription Factor NF-Y. Chembiochem (2024)

Release Date

2024-03-20

Peptides

Nuclear transcription factor Y subunit alpha: A
Nuclear transcription factor Y subunit beta: B
Nuclear transcription factor Y subunit gamma: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Nuclear transcription factor Y subunit alpha

Nuclear transcription factor Y subunit beta

Nuclear transcription factor Y subunit gamma

Related Entries With Identical Sequence