Structure of PDB 4yfu Chain A Binding Site BS01

Receptor Information

>4yfu Chain A (length=579) Species: 1422 (Geobacillus stearothermophilus)

KMAFTLADRVTEEMLADKAALVVEVVEENYHDAPIVGIAVVNEHGRFFLR
PETALADPQFVAWLGDETKKKSMFDSKRAAVALKWKGIELCGVSFDLLLA
AYLLDPAQGVDDVAAAAKMKQYEAVRPDEAVYGKGAKRAVPDEPVLAEHL
VRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAEMEFAGVKVDT
KRLEQMGKELAEQLGTVEQRIYELAGQEFNINSPKQLGVILFEKLQLPVL
KKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRP
ATKKVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDW
LIFAADYSQIELRVLAHIAEDDNLMEAFRRDLDIHTKTAMDIFQVSEDEV
TPNMRRQAKAVNYGIVYGISDYGLAQNLNISRKEAAEFIERYFESFPGVK
RYMENIVQEAKQKGYVTTLLHRRRYLPDITSRNFNVRSFAERMAMNTPIQ
GSAADIIKKAMIDLNARLKEERLQAHLLLQVHDELILEAPKEEMERLCRL
VPEVMEQAVTLRVPLKVDYHYGSTWYDAK

Ligand information

>4yfu Chain B (length=9)

catgatgcu

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4yfu The Closing Mechanism of DNA Polymerase I at Atomic Resolution.
• Resolution: 1.5 Å
• Binding residue (original residue number in PDB): T550 K551 T552 T556 R578 Q579 K582 Y587 R615 Q624 N625 I626 P627 I628 R629 V828 H829 D830
• Binding residue (residue number reindexed from 1): T253 K254 T255 T259 R281 Q282 K285 Y290 R318 Q327 N328 I329 P330 I331 R332 V531 H532 D533

Enzymatic activity

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

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0004518 nuclease activity
• GO:0008408 3'-5' exonuclease activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006139 nucleobase-containing compound metabolic process
• GO:0006260 DNA replication
• GO:0006261 DNA-templated DNA replication
• GO:0006281 DNA repair
• GO:0006302 double-strand break repair
• GO:0006974 DNA damage response
• GO:0071897 DNA biosynthetic process

External links

• PDB: RCSB:4yfu, PDBe:4yfu, PDBj:4yfu
• PDBsum: 4yfu
• PubMed: 26211612
• UniProt: E1C9K5