Structure of PDB 7yd6 Chain B

Receptor sequence

>7yd6B (length=434) Species: 192952 (Methanosarcina mazei Go1) [Search protein sequence]

LVPRGSHMNPKRIRALKSGKQGDGPVVYWMSRDQRAEDNWALLFSRAIAK
EANVPVVVVFCLTDEFLEAGIRQYEFMLKGLQELEVSLSRKKIPSFFLRG
DPGEKISRFVKDYNAGTLVTDFSPLRIKNQWIEKVISGISIPFFEVDAHN
VVPCWEASQKHEYAAHTFRPKLYALLPEFLEEFPELEPNSVTPDPLFEPW
HFEPGEKAAKKVMESFIADRLDSYGALRNDPTKNMLSNLSPYLHFGQISS
QRVVLEVEKAESNPGSKKAFLDEILIWKEISDNFCYYNPGYDGFESFPSW
AKESLNAHRNDVRSHIYTLEEFEAGKTHDPLWNASQMELLSTGKMHGYTR
MYWAKKILEWSESPEKALEIAICLNDRYELDGRDPNGYAGIAWSIGGVHD
RAWGEREVTGKIRYMSYEGCKRKFDVKLYIEKYS

3D structure

PDB

7yd6 Visualizing the DNA repair process by a photolyase at atomic resolution

Chain

Resolution

2.15 Å

3D
structure

[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]

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)
BS01	dna	B	H161 R256 E301 W305 Y376 M379 W421 R429 W431 R441 Y442 M443 R450 K451	H166 R228 E273 W277 Y348 M351 W393 R401 W403 R413 Y414 M415 R422 K423
BS02	dna	B	Y158 R429 W431 K439 R450	Y163 R401 W403 K411 R422
BS03	FAD	B	Y252 L264 S265 N266 S268 L271 E301 I302 W305 K372 R378 N403 D409 N414 G415 S422	Y224 L236 S237 N238 S240 L243 E273 I274 W277 K344 R350 N375 D381 N386 G387 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

View graph for
Molecular Function

View graph for
Biological Process

External links

PDB	RCSB:7yd6, PDBe:7yd6, PDBj:7yd6
PDBsum	7yd6
PubMed	38033054
UniProt	Q8PYK9

[Back to BioLiP]