Structure of PDB 7nkx Chain W

Receptor sequence

>7nkxW (length=622) Species: 559292 (Saccharomyces cerevisiae S288C)

DFHGIDIVINHRLKTSKTVPDLNNCKENYEFLIKWTDESHLHNTWETYES
IGQVRGLKRLDNYCKQFIIEDQQVRLDPYVTAEDIEIMDMERERRLDEFE
EFHVPERIIDSQRASLEDGTSQLQYLVKWRRLNYDEATWENATDIVKLAP
EQVKHFQNRENSKILPQYSSNYTSQRPRFEKLSVQPPFIKGGELRDFQLT
GINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARRQNGPHIIVV
PLSTMPAWLDTFEKWAPDLNCICYMGNQKSRDTIREYEFYTNPKTMKFNV
LLTTYEYILKDRAELGSIKWQFMAVDEAHRLKNAESSLYESLNSFKVANR
MLITGTPLQNNIKELAALVNFLMPGRFNQDEEQEEYIHDLHRRIQPFILR
RLKKDVEKSLPSKTERILRVELSDVQTEYYKNILTKNYSIMNELKKASNH
PYLFDNAEERVLTRENVLRGLIMSSGKMVLLDQLLTRLKKDGHRVLIFSQ
MVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLL
STRAGGLGINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRL
VSKDTVEEEVLERARKKMILEY

3D structure

• PDB: 7nkx Structural basis of nucleosome transcription mediated by Chd1 and FACT.
• Chain: W
• Resolution: 2.9 Å

Enzymatic activity

• Enzyme Commision number: 3.6.4.-

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	dna	W	K240 L434 R463 K497 N653 M720 V721 G743 R750 S770 R772	K58 L252 R281 K310 N442 M501 V502 G524 R531 S551 R553
BS02	dna	W	R241 K519 S523 S524 N547 W793 N794 R832	R59 K332 S336 S337 N360 W574 N575 R613
BS03	ADP	W	E375 G404 L405 G406 K407 T408 W447 R807 I808	E193 G222 L223 G224 K225 T226 W265 R588 I589
BS04	BEF	W	M403 E514 L776 G777 Q800 R804 R807	M221 E327 L557 G558 Q581 R585 R588

Gene Ontology

Molecular Function

• GO:0000182 rDNA binding
• GO:0000976 transcription cis-regulatory region binding
• GO:0003677 DNA binding
• GO:0003682 chromatin binding
• GO:0004386 helicase activity
• GO:0005524 ATP binding
• GO:0008094 ATP-dependent activity, acting on DNA
• GO:0016787 hydrolase activity
• GO:0016887 ATP hydrolysis activity
• GO:0031490 chromatin DNA binding
• GO:0035064 methylated histone binding
• GO:0042393 histone binding
• GO:0097159 organic cyclic compound binding
• GO:0140658 ATP-dependent chromatin remodeler activity

Biological Process

• GO:0000724 double-strand break repair via homologous recombination
• GO:0000729 DNA double-strand break processing
• GO:0001178 regulation of transcriptional start site selection at RNA polymerase II promoter
• GO:0006325 chromatin organization
• GO:0006338 chromatin remodeling
• GO:0006357 regulation of transcription by RNA polymerase II
• GO:0006363 termination of RNA polymerase I transcription
• GO:0006368 transcription elongation by RNA polymerase II
• GO:0006369 termination of RNA polymerase II transcription
• GO:0007062 sister chromatid cohesion
• GO:0009889 regulation of biosynthetic process
• GO:0034728 nucleosome organization
• GO:1902275 regulation of chromatin organization
• GO:2000104 negative regulation of DNA-templated DNA replication

Cellular Component

• GO:0000123 histone acetyltransferase complex
• GO:0000124 SAGA complex
• GO:0000785 chromatin
• GO:0005634 nucleus
• GO:0005739 mitochondrion
• GO:0030874 nucleolar chromatin
• GO:0035861 site of double-strand break
• GO:0046695 SLIK (SAGA-like) complex

External links

• PDB: RCSB:7nkx, PDBe:7nkx, PDBj:7nkx
• PDBsum: 7nkx
• PubMed: 33846633
• UniProt: P32657|CHD1_YEAST Chromo domain-containing protein 1 (Gene Name=CHD1)