Structure of PDB 8kcm Chain A

Receptor sequence

>8kcmA (length=453) Species: 192952 (Methanosarcina mazei Go1)

PRGSHMNPKRIRALKSGKQGDGPVVYWMSRDQRAEDNWALLFSRAIAKEA
NVPVVVVFCLTDEFLEAGIRQYEFMLKGLQELEVSLSRKKIPSFFLRGDP
GEKISRFVKDYNAGTLVTDFSPLRIKNQWIEKVISGISIPFFEVDAHNVV
PCWEASQKHEYAAHTFRPKLYALLPEFLEEFPELEPNSVTLSDVLETGVK
ALLPERALLKNKDPLFEPWHFEPGEKAAKKVMESFIADRLDSYGALRNDP
TKNMLSNLSPYLHFGQISSQRVVLEVEKAESNPGSKKAFLDEILIWKEIS
DNFCYYNPGYDGFESFPSWAKESLNAHRNDVRSHIYTLEEFEAGKTHDPL
WNASQMELLSTGKMHGYTRMYWAKKILEWSESPEKALEIAICLNDRYELD
GRDPNGYAGIAWSIGGVHDRAWGEREVTGKIRYMSYEGCKRKFDVKLYIE
KYS

3D structure

• PDB: 8kcm Visualizing the DNA repair process by a photolyase at atomic resolution
• Chain: A
• Resolution: 2.5 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	A	A160 H161 R256 N257 E301 W305 Y376 M379 W421 R429 W431 R441 Y442 M443 S444 K451	A163 H164 R247 N248 E292 W296 Y367 M370 W412 R420 W422 R432 Y433 M434 S435 K442
BS02	dna	A	Y158 R429 A430 W431 G432 E433 K439	Y161 R420 A421 W422 G423 E424 K430
BS03	FAD	A	Y252 L264 S265 N266 S268 F298 E301 I302 W305 K306 K372 R378 N403 D409 N414 G415 G418	Y243 L255 S256 N257 S259 F289 E292 I293 W296 K297 K363 R369 N394 D400 N405 G406 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

External links

• PDB: RCSB:8kcm, PDBe:8kcm, PDBj:8kcm
• PDBsum: 8kcm
• PubMed: 38033054
• UniProt: Q8PYK9