Structure of PDB 3mdc Chain A

Receptor sequence

>3mdcA (length=312) Species: 9606 (Homo sapiens)

LHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIP
GIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWY
QQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAA
QAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQ
EGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACAL
LYFTGSAHFNRSMRALAKTKGMSLSEHALSTAGPGRVLPTPTEKDVFRLL
GLPYREPAERDW

3D structure

• PDB: 3mdc Interaction between DNA Polymerase lambda and anticancer nucleoside analogs.
• Chain: A
• Resolution: 1.999 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D427 D429 D490
• Catalytic site (residue number reindexed from 1): D174 D176 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 Q372 V462 S463 Q464 Q471 K472 R514 R517 K521 L527 S528 E529 H530	W21 Q119 V209 S210 Q211 Q218 K219 R261 R264 K268 L274 S275 E276 H277
BS02	dna	A	W342 G343 G345 K347 T348 R488 D490 Y505	W89 G90 G92 K94 T95 R235 D237 Y252
BS03	dna	A	W274 R275 G278 Y279 G304 G306 R308 M309	W21 R22 G25 Y26 G51 G53 R55 M56
BS04	GTF	A	R386 G416 S417 R420 C425 G426 D427 D429 Y505 F506 T507 G508 A510 N513	R133 G163 S164 R167 C172 G173 D174 D176 Y252 F253 T254 G255 A257 N260
BS05	MG	A	D427 D429 D490	D174 D176 D237
BS06	MG	A	D427 D429	D174 D176

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:3mdc, PDBe:3mdc, PDBj:3mdc
• PDBsum: 3mdc
• PubMed: 20348107
• UniProt: Q9UGP5|DPOLL_HUMAN DNA polymerase lambda (Gene Name=POLL)