Structure of PDB 3kd5 Chain E

Receptor sequence

>3kd5E (length=905) Species: 12353 (Escherichia phage RB69)

MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYF
DIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYE
IKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFD
LLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLME
YLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGESTAKRLSPHRKTRV
KVIENMYGSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNV
GKLKYDGPISKLRESNHQRYISYNIIDVYRVLQIDAKRQFINLSLDMGYY
AKIQIQSVFSPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPI
PNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERP
SDVYSCSPNGMMYYKDRDGVVPTEITKWVSQRKEHKGYMLAAQRNGEIIK
EALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEV
AGMTAQMALKVTCNSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERK
VNEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDF
LDKFARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGG
FWTGKKRYALNVWDMEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIR
RMLQEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPK
CPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPS
GTEITDLIKDDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDM
FDFSA

3D structure

• PDB: 3kd5 Phosphonoformic acid inhibits viral replication by trapping the closed form of the DNA polymerase.
• Chain: E
• Resolution: 2.69 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	E	E219 I253 R260 I262 D275 S357 F359 S360 P361 I362 Y391 P392 G393 A394 S565 G568 N572 W574 K705 R707 C801 K844 K874	E219 I253 R260 I262 D275 S357 F359 S360 P361 I362 Y391 P392 G393 A394 S565 G568 N572 W574 K705 R707 C801 K844 K874
BS02	dna	E	N284 D411 Y416 K560 N564 Y567 T622 D623 K706 Y708 M728 G729 K734 S735 S783 S784 N786 Y791 H804	N284 D411 Y416 K560 N564 Y567 T622 D623 K706 Y708 M728 G729 K734 S735 S783 S784 N786 Y791 H804
BS03	PPF	E	L412 T413 S414 R482 K560	L412 T413 S414 R482 K560
BS04	MG	E	D411 D623	D411 D623
BS05	MG	E	D411 L412 D623	D411 L412 D623
BS06	MG	E	D114 E116 D327	D114 E116 D327

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:3kd5, PDBe:3kd5, PDBj:3kd5
• PDBsum: 3kd5
• PubMed: 21566148
• UniProt: Q38087|DPOL_BPR69 DNA-directed DNA polymerase (Gene Name=43)