Structure of PDB 5dkw Chain B

Receptor sequence

>5dkwB (length=319) Species: 9606 (Homo sapiens)

ATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQE
ACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKT
AQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQT
VQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLL
DSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSE
FACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVGPGRVLPTPTE
KDVFRLLGLPYREPAERDW

3D structure

• PDB: 5dkw Structural Mechanism for the Fidelity Modulation of DNA Polymerase lambda
• Chain: B
• Resolution: 2.689 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D427 D429 D490
• Catalytic site (residue number reindexed from 1): D179 D181 D242
• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.
  4.2.99.-

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	Y267 W274 R275 Y279 P303 G304 G306 R308 M309 K312	Y19 W26 R27 Y31 P55 G56 G58 R60 M61 K64
BS02	dna	B	W342 G343 G345 K347 T348	W94 G95 G97 K99 T100
BS03	dna	B	W274 Q372 E465 E466 R514 R517 K521	W26 Q124 E217 E218 R266 R269 K273
BS04	CA	B	C300 I302 I305	C52 I54 I57
BS05	CA	B	S339 I341 A344	S91 I93 A96
BS06	DTP	B	R386 S417 G426 D427 Y505 G508	R138 S169 G178 D179 Y257 G260
BS07	CA	B	D427 D429	D179 D181

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0016779 nucleotidyltransferase activity
• GO:0034061 DNA polymerase activity

Biological Process

• GO:0006281 DNA repair

External links

• PDB: RCSB:5dkw, PDBe:5dkw, PDBj:5dkw
• PDBsum: 5dkw
• PubMed: 26836966
• UniProt: Q9UGP5|DPOLL_HUMAN DNA polymerase lambda (Gene Name=POLL)