SMTL ID : 7ah8.1

NF-Y bound to suramin inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-2-2-mer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain B: P.4, L.5 Chain D: Q.1, L.5 Ligands: SVR.3 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:L.5, D:Q.1

1 x FLC: CITRATE ANION(Non-functional Binders)

FLC.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x SVR: 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID(Non-covalent)

SVR.3: 26 residues within 4Å: Chain A: F.88, R.89 Chain B: L.5, K.9, K.13, K.19, M.20, I.21, S.22, A.23, E.24, P.26 Chain C: F.88, R.89 Chain D: Q.1, L.5, K.9, K.13, K.19, M.20, I.21, S.22, A.23, E.24, P.26 Ligands: GOL.1 25 PLIP interactions: 10 interactions with chain D, 9 interactions with chain B, 3 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: D:K.9, D:A.23, D:P.26, B:I.21, B:A.23, B:P.26, A:F.88 Hydrogen bonds: D:K.19, D:I.21, D:I.21, B:K.9, B:I.21, B:E.24 Salt bridges: D:K.9, D:K.13, D:K.13, B:K.9, B:K.13, A:R.89, C:R.89 pi-Cation interactions: D:K.9, B:K.9, A:R.89, C:R.89 pi-Stacking: C:F.88

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nardone, V. et al., Structural Basis of Inhibition of the Pioneer Transcription Factor NF-Y by Suramin. Cells (2020)

Release Date

2021-08-04

Peptides

Nuclear transcription factor Y subunit beta: AC
Isoform 6 of Nuclear transcription factor Y subunit gamma: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Nuclear transcription factor Y subunit beta

Isoform 6 of Nuclear transcription factor Y subunit gamma