Structure of PDB 6ras Chain I

Receptor sequence

>6rasI (length=433) Species: 74545 (Prochlorococcus marinus str. MIT 9302)

ELFKEEIIHQLELHPSRLDKEKIISEAMEDGIDDFFEGIRMALDPLVTFG
VKIVPEKESEKSQNFLWEDFRKLANKLMQRELTGHAARDAILTAMESATK
EEWNGFYRRVLIKDLACGVSEKTINKIAKKFPKYAIPIFSCPLAHDSANH
EKKMIGKKQIEIKLDGVRVLTIIRQNKVEMFSRNGKQFHNFGHIILEIEN
VLKEDPAPYDLVLDGEVMSANFQDLMKQVHRKDGKQTKDAVLHLFDLCPL
ENFQKGRWNTKQTARSLLVKKWVAKHSLLLKHIQTLEWENVDLDTIQGQK
RFVELNKSAVEGGYEGVMIKDPDGMYECKRTHSWLKAKPFIEVTLKVVSV
EEGTGRNKGRLGAILVEGEDDGYEYSLSCGSGFSDIQREEYWSKRKHLLG
QLVEIRADAKTKSKDGVAFSLRFPRFKCFRGFK

3D structure

• PDB: 6ras Structural intermediates of a DNA-ligase complex illuminate the role of the catalytic metal ion and mechanism of phosphodiester bond formation.
• Chain: I
• Resolution: 2.75 Å

Enzymatic activity

• Enzyme Commision number: 6.5.1.1: DNA ligase (ATP).

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	I	T87 H89 G122 K126 T127 Q227 M230 K231 R235 K236 G357 T358 R360 N361 G366 A367 S382 T415 K416 S417 K418 S424 L425 F427	T83 H85 G118 K122 T123 Q223 M226 K227 R231 K232 G353 T354 R356 N357 G362 A363 S378 T411 K412 S413 K414 S420 L421 F423
BS02	dna	I	G54 K56 G170 V171 R172 S186 R187 N188 K190 F226 H234 F427	G50 K52 G166 V167 R168 S182 R183 N184 K186 F222 H230 F423
BS03	dna	I	S20 R21 L22 K340 K342 S385 D389 F427 R429	S16 R17 L18 K336 K338 S381 D385 F423 R425
BS04	AMP	I	K167 L168 R172 E220 F249 M322 K324 K340	K163 L164 R168 E216 F245 M318 K320 K336

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003909 DNA ligase activity
• GO:0003910 DNA ligase (ATP) activity
• GO:0005524 ATP binding
• GO:0016874 ligase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006260 DNA replication
• GO:0006281 DNA repair
• GO:0006310 DNA recombination

External links

• PDB: RCSB:6ras, PDBe:6ras, PDBj:6ras
• PDBsum: 6ras
• PubMed: 31312841
• UniProt: A0A0A2ACP7