Structure of PDB 5o9g Chain W

Receptor sequence

>5o9gW (length=855) Species: 559292 (Saccharomyces cerevisiae S288C)

DFHGIDIVINHRLKTSKTVPDLNNCKENYEFLIKWTDESHLHNTWETYES
IGQVRGLKRLDNYCKQFIIEDQQVRLDPYVTAEDIEIMDMERERRLDEFE
EFHVPERIIDSQRASLEDGTSQLQYLVKWRRLNYDEATWENATDIVKLAP
EQVKHFQNRENSKILPQYSSNYTSQRPRFEKLSVQPPFIKGGELRDFQLT
GINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARRQNGPHIIVV
PLSTMPAWLDTFEKWAPDLNCICYMGNQKSRDTIREYEFYTNPKTMKFNV
LLTTYEYILKDRAELGSIKWQFMAVDEAHRLKNAESSLYESLNSFKVANR
MLITGTPLQNNIKELAALVNFLMPGRFNQDEEQEEYIHDLHRRIQPFILR
RLKKDVEKSLPSKTERILRVELSDVQTEYYKNILTKNYSIMNELKKASNH
PYLFDNAEERVLQKFMTRENVLRGLIMSSGKMVLLDQLLTRLKKDGHRVL
IFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDF
VFLLSTRAGGLGINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVM
VYRLVSKDTVEEEVLERARKKMILEYDMDSIGESEVRALYKAILKFGNLK
EILDELIADGTLPVKSFEKYGETYDEMMEAAKDCVHEEEKNRKEILEKLE
KHATAYRAKLKSGEIKAENQPKDNPLTRLSLKKREKKAVLFNFKGVKSLN
AESLLSRVEDLKYLKNLINSNYKDDPLKFSLGNNTPKPVQNWSSNWTKEE
DEKLLIGVFKYGYGSWTQIRDDPFLGITDKIFLKKVPGAIHLGRRVDYLL
SFLRG

3D structure

• PDB: 5o9g Nucleosome-Chd1 structure and implications for chromatin remodelling.
• Chain: W
• Resolution: 4.8 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 N459 E493 K497 N653 Q719 M720 V721 R772 A773 K1115	K58 L252 N277 E306 K310 N442 Q504 M505 V506 R557 A558 K736
BS02	dna	W	R241 L496 K519 S523 S524 R772 W793 R1016 H1252 R1255	R59 L309 K332 S336 S337 R557 W578 R637 H841 R844
BS03	ADP	W	R377 G406 T408 V409 W447 N779 M781 R807	R195 G224 T226 V227 W265 N564 M566 R592
BS04	BEF	W	M403 E514 R804 R807	M221 E327 R589 R592

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:5o9g, PDBe:5o9g, PDBj:5o9g
• PDBsum: 5o9g
• PubMed: 29019976
• UniProt: P32657|CHD1_YEAST Chromo domain-containing protein 1 (Gene Name=CHD1)