Structure of PDB 5w2c Chain B

Receptor sequence

>5w2cB (length=431) Species: 9606 (Homo sapiens)

LDKEKINKIIMEATKGSRFYGNELKKEKQVNQRIENMMQQKAQITSQQLR
KAQLQVDRFAMELEQSRNLSNTIVHIDMDAFYAAVEMRDNPELKDKPIAV
GSMSMLSTSNYHARRFGVRAAMPGFIAKRLCPQLIIVPPNFDKYRAVSKE
VKEILADYDPNFMAMSLDEAYLNITKHLEERQNWPEDKRRYFIKNSVVFG
TSAQEVVKEIRFRIEQKTTLTASAGIAPNTMLAKVCSDKNKPNGQYQILP
NRQAVMDFIKDLPIRKVSGIGKVTEKMLKALGIITCTELYQQRALLSLLF
SETSWHYFLHISLGLGSTHLTRDGERKSMSVERTFSEINKAEEQYSLCQE
LCSELAQDLQKERLKGRTVTIKLKNVNFEVKTRASTVSSVVSTAEEIFAI
AKELLKTEIDADFPHPLRLRLMGVRISSFPN

3D structure

• PDB: 5w2c Mechanism of Error-Free DNA Replication Past Lucidin-Derived DNA Damage by Human DNA Polymerase kappa.
• Chain: B
• Resolution: 2.5 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 S196 K321 S355 G356 G358 V360 T361 R454 T469 R470 A471 S472 T473	R33 S166 K234 S268 G269 G271 V273 T274 R367 T382 R383 A384 S385 T386
BS02	dna	B	T44 F49 S134 M135 P153 F155 I156 S388 R413 K414 S415 S417 V418 E419 T421 R507	T14 F19 S104 M105 P123 F125 I126 S301 R326 K327 S328 S330 V331 E332 T334 R420
BS03	MG	B	D107 M108 D198	D77 M78 D168
BS04	MG	B	R352 I357	R265 I270
BS05	MG	B	D107 D198 E199	D77 D168 E169
BS06	DZ4	B	D107 M108 A110 F111 Y112 S137 T138 Y141 R144 D198 K328	D77 M78 A80 F81 Y82 S107 T108 Y111 R114 D168 K241

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:5w2c, PDBe:5w2c, PDBj:5w2c
• PDBsum: 5w2c
• PubMed: 28972744
• UniProt: Q9UBT6|POLK_HUMAN DNA polymerase kappa (Gene Name=POLK)