Structure of PDB 4ds5 Chain D Binding Site BS01

Receptor Information

>4ds5 Chain D (length=561) Species: 235909 (Geobacillus kaustophilus HTA426)

LAKMAFTLADRVTEEMLADKAALVVEVVEENYHDAPIVGIAVVNEHGRFF
LRPETALADPQFVAWLGDETKKKSMFDSKRAAVALKWKGIELCGVSFDLL
LAAYLLDPAQGVDDVAAAAKMKQYEAVRPDEAVYGKGAKRAVPDEPVLAE
HLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAEMEFAGVKV
DTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSPKQLGVILFEKLQLP
VLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVV
RPATKKVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSES
DWLIFAADYSQIELRVLAHIAEDDNLMEAFRRDLDIHTKTKAVNFGIVYG
ISDYGLAQNLNISRKEAAEFIERYFESFPGVKRYMENIVQEAKQKGYVTT
LLHRRRYLPDITSRNFNVRSFAERMAMNTPIQGSAADIIKKAMIDLNARL
KEERLQAHLLLQVHDELILEAPKEEMERLCRLVPEVMEQAVTLRVPLKVD
YHYGSTWYDAK

Ligand information

>4ds5 Chain E (length=9)

cctgactcc

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4ds5 Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides.
• Resolution: 1.68 Å
• Binding residue (original residue number in PDB): T550 K551 T552 T556 A558 R578 K582 Y587 R615 Q624 N625 I626 P627 I628 R629 H829
• Binding residue (residue number reindexed from 1): T255 K256 T257 T261 A263 R283 K287 Y292 R320 Q329 N330 I331 P332 I333 R334 H514

Enzymatic activity

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

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0008408 3'-5' exonuclease activity

Biological Process

• GO:0006139 nucleobase-containing compound metabolic process
• GO:0006260 DNA replication
• GO:0006261 DNA-templated DNA replication

External links

• PDB: RCSB:4ds5, PDBe:4ds5, PDBj:4ds5
• PDBsum: 4ds5
• PubMed: 22648417
• UniProt: Q5KWC1