Structure of PDB 3ndk Chain A

Receptor sequence

>3ndkA (length=903) Species: 12353 (Escherichia phage RB69)

MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYF
DIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYE
IKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFD
LLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLME
YLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGESTAKRLSPHRKTRV
KVIENMYGSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNV
GKLKYDGPISKLRESNHQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYY
AKIQIQSVFSPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPI
PNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERP
SDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIK
EALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEV
AGMTAQINRKLLINSLAGALGNVWFRYYDLRNATAITTFGQMALQWIERK
VNEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDF
LDKFARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGG
FWTGKKRYALNVWDMEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIR
RMLQEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPK
CPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPS
GTEITDLIKDDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDM
FDF

3D structure

• PDB: 3ndk Variation in Mutation Rates Caused by RB69pol Fidelity Mutants Can Be Rationalized on the Basis of Their Kinetic Behavior and Crystal Structures.
• Chain: A
• Resolution: 2.0 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	E219 I253 E254 R260 F359 S360 P361 I362 Y391 P392 G393 A394 N564 S565 G568 N572 K705 K706 R707 S784 N786 K800 F803 K844 K874	E219 I253 E254 R260 F359 S360 P361 I362 Y391 P392 G393 A394 N564 S565 G568 N572 K705 K706 R707 S784 N786 K800 F803 K844 K874	PDBbind-CN: Kd=68uM
BS02	dna	A	N284 D621 K706 Y708 M728 G729 K734 S735 S783 S784 N786 Y791 K800 H804	N284 D621 K706 Y708 M728 G729 K734 S735 S783 S784 N786 Y791 K800 H804	PDBbind-CN: Kd=68uM
BS03	DCP	A	D411 S414 L415 Y416 R482 K560 N564 T622 D623	D411 S414 L415 Y416 R482 K560 N564 T622 D623
BS04	CA	A	D411 L412 D623	D411 L412 D623
BS05	CA	A	D411 D623	D411 D623
BS06	CA	A	N505 N507 K531	N505 N507 K531
BS07	CA	A	D411 E686 E716	D411 E686 E716

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:3ndk, PDBe:3ndk, PDBj:3ndk
• PDBsum: 3ndk
• PubMed: 21216248
• UniProt: Q38087|DPOL_BPR69 DNA-directed DNA polymerase (Gene Name=43)