Structure of PDB 3pzp Chain B

Receptor sequence

>3pzpB (length=443) Species: 9606 (Homo sapiens)

MGLNDNKAGMEGLDKEKINKIIMEATKGSRFYGNELKKEKQVNQRIENMM
QQKAQITSQQLRKAQLQVDRFAMELEQSRNLSNTIVHIDMDAFYAAVEMR
DNPELKDKPIAVGSMSMLSTSNYHARRFGVRAAMPGFIAKRLCPQLIIVP
PNFDKYRAVSKEVKEILADYDPNFMAMSLDEAYLNITKHLEERQNWPEDK
RRYFIKNSVVFGTSAQEVVKEIRFRIEQKTTLTASAGIAPNTMLAKVCSD
KNKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKMLKALGIITCTE
LYQQRALLSLLFSETSWHYFLHISLGLGSTHLTRDGERKSMSVERTFSEI
NKAEEQYSLCQELCSELAQDLQKERLKGRTVTIKLKNVNFEVKTRASTVS
SVVSTAEEIFAIAKELLKTEIDADFPHPLRLRLMGVRISSFPN

3D structure

• PDB: 3pzp Role of human DNA polymerase kappa in extension opposite from a cis-syn thymine dimer.
• Chain: B
• Resolution: 3.336 Å

Enzymatic activity

• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.

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	E199 G356 G358 T361 R454 K468 T469 R470 A471 T473	E181 G281 G283 T286 R379 K393 T394 R395 A396 T398
BS02	dna	B	F49 M135 P153 I156 S388 T390 R413 K414 S415 M416 S417 E419 T421 R507	F31 M117 P135 I138 S313 T315 R338 K339 S340 M341 S342 E344 T346 R432
BS03	DTP	B	M108 A110 Y112 S137 T138 Y141 R144 D198 K328	M90 A92 Y94 S119 T120 Y123 R126 D180 K253
BS04	MG	B	R352 I357	R277 I282

Gene Ontology

Molecular Function

• GO:0003684 damaged DNA binding
• GO:0003887 DNA-directed DNA polymerase activity

Biological Process

• GO:0006281 DNA repair

External links

• PDB: RCSB:3pzp, PDBe:3pzp, PDBj:3pzp
• PDBsum: 3pzp
• PubMed: 21354175
• UniProt: Q9UBT6|POLK_HUMAN DNA polymerase kappa (Gene Name=POLK)