Structure of PDB 3in5 Chain B

Receptor sequence

>3in5B (length=437) Species: 9606 (Homo sapiens)

NDNKAGMEGLDKEKINKIIMEATKGSRFYGNELKKEKQVNQRIENMMQQK
AQITSQQLRKAQLQVDRFAMELEQSRNLSNTIVHIDMDAFYAAVEMRDNP
ELKDKPIAVGSMSMLSTSNYHARRFGVRAAMPGFIAKRLCPQLIIVPPNF
DKYRAVSKEVKEILADYDPNFMAMSLDEAYLNITKHLEERQNWPEDKRRY
FIVVFGTSAQEVVKEIRFRIEQKTTLTASAGIAPNTMLAKVCSDKNKPNG
QYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKMLKALGIITCTELYQQRA
LLSLLFSETSWHYFLHISLGLGSTHLTRDGERKSMSVERTFSEINKAEEQ
YSLCQELCSELAQDLQKERLKGRTVTIKLKNVNFEVKTRASTVSSVVSTA
EEIFAIAKELLKTEIDADFPHPLRLRLMGVRISSFPN

3D structure

• PDB: 3in5 Structure of human DNA polymerase kappa inserting dATP opposite an 8-oxoG DNA lesion
• Chain: B
• Resolution: 3.2 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	R63 E199 K321 G356 I357 G358 V360 T361 R454 R470 A471 S472 T473	R42 E178 K240 G275 I276 G277 V279 T280 R373 R389 A390 S391 T392
BS02	dna	B	T44 F49 S134 M135 A151 P153 T390 R413 K414 S415 M416 S417 V418 E419 R420 T421 R507	T23 F28 S113 M114 A130 P132 T309 R332 K333 S334 M335 S336 V337 E338 R339 T340 R426
BS03	ATP	B	D107 M108 A110 F111 Y112 S137 T138 Y141 R144 D198 K328	D86 M87 A89 F90 Y91 S116 T117 Y120 R123 D177 K247
BS04	MG	B	D107 M108 D198	D86 M87 D177
BS05	MG	B	R352 V354 I357	R271 V273 I276

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:3in5, PDBe:3in5, PDBj:3in5
• PDBsum: 3in5
• PubMed: 19492058
• UniProt: Q9UBT6|POLK_HUMAN DNA polymerase kappa (Gene Name=POLK)