Structure of PDB 3pml Chain B

Receptor sequence

>3pmlB (length=324) Species: 9606 (Homo sapiens)

QKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSY
QEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGT
KTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIE
QTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSR
LLDSLRQEGFLTDDLVKGETKYLGVCRLPGPGRRHRRLDIIVVPYSEFAC
ALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVL
PTPTEKDVFRLLGLPYREPAERDW

3D structure

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

Enzymatic activity

• Catalytic site (original residue number in PDB): D427 D429 D490
• Catalytic site (residue number reindexed from 1): D181 D183 D239
• 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	W274 K463 R517	W28 K217 R266
BS02	dna	B	W342 G343 A344 G345 T346 K347 T348 Y505	W96 G97 A98 G99 T100 K101 T102 Y254
BS03	dna	B	Y267 W274 R275 G278 Y279 G304 I305 G306 R308 M309 K312	Y21 W28 R29 G32 Y33 G58 I59 G60 R62 M63 K66
BS04	dna	B	V537 R549	V286 R298
BS05	1GC	B	R386 G416 S417 D427 D429 Y505 F506 T507 G508 N513	R140 G170 S171 D181 D183 Y254 F255 T256 G257 N262
BS06	MG	B	D427 D429	D181 D183
BS07	MG	B	D427 D429 D490	D181 D183 D239

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)