Structure of PDB 7yd8 Chain A

Receptor sequence

>7yd8A (length=456) Species: 192952 (Methanosarcina mazei Go1) [Search protein sequence]

PRGSHMNPKRIRALKSGKQGDGPVVYWMSRDQRAEDNWALLFSRAIAKEA
NVPVVVVFCLTDEFLEAGIRQYEFMLKGLQELEVSLSRKKIPSFFLRGDP
GEKISRFVKDYNAGTLVTDFSPLRIKNQWIEKVISGISIPFFEVDAHNVV
PCWEASQKHEYAAHTFRPKLYALLPEFLEEFPELEPNSVTPETLSDVLET
GVKALLPERALLKNKDPLFEPWHFEPGEKAAKKVMESFIADRLDSYGALR
NDPTKNMLSNLSPYLHFGQISSQRVVLEVEKAESNPGSKKAFLDEILIWK
EISDNFCYYNPGYDGFESFPSWAKESLNAHRNDVRSHIYTLEEFEAGKTH
DPLWNASQMELLSTGKMHGYTRMYWAKKILEWSESPEKALEIAICLNDRY
ELDGRDPNGYAGIAWSIGGVHDRAWGEREVTGKIRYMSYEGCKRKFDVKL
YIEKYS

3D structure

PDB

7yd8 Visualizing the DNA repair process by a photolyase at atomic resolution

Chain

Resolution

2.15 Å

3D
structure

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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	A	A160 H161 R256 E301 W305 Y376 M379 W421 R429 W431 R441 Y442 S444 K451	A163 H164 R250 E295 W299 Y370 M373 W415 R423 W425 R435 Y436 S438 K445
BS02	dna	A	Y158 T162 W328 R429 A430 W431 G432 E433 K439	Y161 T165 W322 R423 A424 W425 G426 E427 K433
BS03	FAD	A	Y252 L264 S265 N266 S268 L271 E301 W305 K306 K372 R378 N403 D409 N414 G415	Y246 L258 S259 N260 S262 L265 E295 W299 K300 K366 R372 N397 D403 N408 G409

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:7yd8, PDBe:7yd8, PDBj:7yd8
PDBsum	7yd8
PubMed	38033054
UniProt	Q8PYK9

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