Structure of PDB 3mda Chain A

Receptor sequence

>3mdaA (length=325) Species: 9606 (Homo sapiens)

AHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEAC
SIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQ
MWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQ
KAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDS
LRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFA
CALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRV
LPTPTEKDVFRLLGLPYREPAERDW

3D structure

• PDB: 3mda Interaction between DNA Polymerase lambda and anticancer nucleoside analogs.
• Chain: A
• Resolution: 2.031 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D427 D429 D490
• Catalytic site (residue number reindexed from 1): D177 D179 D240
• 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 S463 Q464 Q471 K472 R514 R517 K521 L527 S528 E529 H530 H541 K544	W24 V212 S213 Q214 Q221 K222 R264 R267 K271 L277 S278 E279 H280 H291 K294
BS02	dna	A	W342 G343 G345 K347 T348 D427 D429 D490 Y505 F506 T507 G508 S509 A510 N513	W92 G93 G95 K97 T98 D177 D179 D240 Y255 F256 T257 G258 S259 A260 N263
BS03	dna	A	W274 R275 G278 Y279 P303 G304 I305 G306 R308 M309 K312	W24 R25 G28 Y29 P53 G54 I55 G56 R58 M59 K62
BS04	MG	A	D427 D429	D177 D179

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