Structure of PDB 7yd7 Chain B

Receptor sequence

>7yd7B (length=434) Species: 192952 (Methanosarcina mazei Go1)

LVPRGSHMNPKRIRALKSGKQGDGPVVYWMSRDQRAEDNWALLFSRAIAK
EANVPVVVVFCLTDEFLEAGIRQYEFMLKGLQELEVSLSRKKIPSFFLRG
DPGEKISRFVKDYNAGTLVTDFSPLRIKNQWIEKVISGISIPFFEVDAHN
VVPCWEASQKHEYAAHTFRPKLYALLPEFLEEFPELEPNSVTPDPLFEPW
HFEPGEKAAKKVMESFIADRLDSYGALRNDPTKNMLSNLSPYLHFGQISS
QRVVLEVEKAESNPGSKKAFLDEILIWKEISDNFCYYNPGYDGFESFPSW
AKESLNAHRNDVRSHIYTLEEFEAGKTHDPLWNASQMELLSTGKMHGYTR
MYWAKKILEWSESPEKALEIAICLNDRYELDGRDPNGYAGIAWSIGGVHD
RAWGEREVTGKIRYMSYEGCKRKFDVKLYIEKYS

3D structure

• PDB: 7yd7 Visualizing the DNA repair process by a photolyase at atomic resolution
• Chain: B
• Resolution: 2.25 Å

Enzymatic activity

• Enzyme Commision number: 4.1.99.3: deoxyribodipyrimidine photo-lyase.

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	B	A160 H161 R256 N257 E301 W305 Y376 M379 W421 R429 W431 R441 Y442 M443 S444 R450 K451	A165 H166 R228 N229 E273 W277 Y348 M351 W393 R401 W403 R413 Y414 M415 S416 R422 K423
BS02	dna	B	Y158 T162 W328 R429 W431 E433 K439 R450	Y163 T167 W300 R401 W403 E405 K411 R422
BS03	FAD	B	Y252 S265 N266 S268 E301 I302 W305 K306 K372 R378 N403 D409 N414 G415 G418 S422	Y224 S237 N238 S240 E273 I274 W277 K278 K344 R350 N375 D381 N386 G387 G390 S394

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003677 DNA binding
• GO:0003904 deoxyribodipyrimidine photo-lyase activity
• GO:0016829 lyase activity

Biological Process

• GO:0000719 photoreactive repair
• GO:0006281 DNA repair

External links

• PDB: RCSB:7yd7, PDBe:7yd7, PDBj:7yd7
• PDBsum: 7yd7
• PubMed: 38033054
• UniProt: Q8PYK9