Structure of PDB 1clq Chain A

Receptor sequence

>1clqA (length=903) Species: 12353 (Escherichia phage RB69)

MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYF
DIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYE
IKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFD
LLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLME
YLNFWQQKTPVILTGWNVESFDIPYVYNRIKNIFGESTAKRLSPHRKTRV
KVIENMYGSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNV
GKLKYDGPISKLRESNHQRYISYNIIDVYRVLQIDAKRQFINLSLDMGYY
AKIQIQSVFSPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPI
PNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERP
SDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIK
EALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEV
AGMTAQINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERK
VNEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDF
LDKFARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGG
FWTGKKRYALNVWDMEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIR
RMLQEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPK
CPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPS
GTEITDLIKDDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDM
FDF

3D structure

• PDB: 1clq Building a replisome from interacting pieces: sliding clamp complexed to a peptide from DNA polymerase and a polymerase editing complex.
• Chain: A
• Resolution: 2.7 Å

Enzymatic activity

• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.
  3.1.11.-

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	A	S220 I253 E254 N255 G258 R260 K734 S736	S220 I253 E254 N255 G258 R260 K734 S736
BS02	dna	A	E116 V117 F123 N217 F221 N255 M256 R260 S287 Y288 S289 L290 I309 Y791	E116 V117 F123 N217 F221 N255 M256 R260 S287 Y288 S289 L290 I309 Y791
BS03	CA	A	N505 N507 K531	N505 N507 K531
BS04	CA	A	E219 D275	E219 D275
BS05	CA	A	C671 N676	C671 N676
BS06	CA	A	D411 D621 D623	D411 D621 D623
BS07	GDP	A	S36 F38 K48 Y49 G84 M85 F370 K378 V379 I380	S36 F38 K48 Y49 G84 M85 F370 K378 V379 I380

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:0004527 exonuclease activity
• GO:0008408 3'-5' exonuclease activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006260 DNA replication
• GO:0006261 DNA-templated DNA replication
• GO:0039686 bidirectional double-stranded viral DNA replication
• GO:0039693 viral DNA genome replication

External links

• PDB: RCSB:1clq, PDBe:1clq, PDBj:1clq
• PDBsum: 1clq
• PubMed: 10535734
• UniProt: Q38087|DPOL_BPR69 DNA-directed DNA polymerase (Gene Name=43)