Structure of PDB 3pml Chain A

Receptor sequence

>3pmlA (length=322) Species: 9606 (Homo sapiens)

ATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQE
ACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKT
AQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQT
VQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLL
DSLRQEGFLTDDLVKGETKYLGVCRLPGPGRRHRRLDIIVVPYSEFACAL
LYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPT
PTEKDVFRLLGLPYREPAERDW

3D structure

• PDB: 3pml Replication infidelity via a mismatch with Watson-Crick geometry.
• Chain: A
• Resolution: 2.6 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D427 D429 D490
• Catalytic site (residue number reindexed from 1): D179 D181 D237
• 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	A	W274 V462 K463 G464 K472 R514 R517 K521 L527 S528	W26 V214 K215 G216 K219 R261 R264 K268 L274 S275
BS02	dna	A	Y267 W274 R275 G278 Y279 P303 G304 G306 R308 M309 K312	Y19 W26 R27 G30 Y31 P55 G56 G58 R60 M61 K64
BS03	dna	A	W342 G343 A344 G345 K347 T348 R488 D490 Y505	W94 G95 A96 G97 K99 T100 R235 D237 Y252
BS04	1GC	A	R386 G416 S417 R420 C425 G426 D427 D429 Y505 F506 T507 G508 N513 R517	R138 G168 S169 R172 C177 G178 D179 D181 Y252 F253 T254 G255 N260 R264
BS05	MG	A	D427 D429	D179 D181
BS06	MG	A	D427 D429 D490	D179 D181 D237

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:3pml, PDBe:3pml, PDBj:3pml
• PDBsum: 3pml
• PubMed: 21233421
• UniProt: Q9UGP5|DPOLL_HUMAN DNA polymerase lambda (Gene Name=POLL)