Lineage for d2dy4d1 (2dy4 D:1-375)

  1. Root: SCOP 1.75
  2. 814173Class c: Alpha and beta proteins (a/b) [51349] (147 folds)
  3. 835945Fold c.55: Ribonuclease H-like motif [53066] (7 superfamilies)
    3 layers: a/b/a; mixed beta-sheet of 5 strands, order 32145; strand 2 is antiparallel to the rest
  4. 836757Superfamily c.55.3: Ribonuclease H-like [53098] (14 families) (S)
    consists of one domain of this fold
  5. 837032Family c.55.3.5: DnaQ-like 3'-5' exonuclease [53118] (15 proteins)
    contains Pfam PF00929
  6. 837033Protein Exonuclease domain of family B DNA polymerases [53125] (8 species)
    elaborated with additional structures and the N-terminal subdomain
  7. 837046Species Bacteriophage RB69 [TaxId:12353] [53127] (15 PDB entries)
    additional N-terminal subdomain contains rudimental OB-fold and rudimental ferredoxin-like fold
  8. 837053Domain d2dy4d1: 2dy4 D:1-375 [131888]
    Other proteins in same PDB: d2dy4a2, d2dy4b2, d2dy4c2, d2dy4d2
    automatically matched to d1clqa1
    complexed with ctg; mutant

Details for d2dy4d1

PDB Entry: 2dy4 (more details), 2.65 Å

PDB Description: crystal structure of rb69 gp43 in complex with dna containing thymine glycol
PDB Compounds: (D:) DNA polymerase

SCOP Domain Sequences for d2dy4d1:

Sequence, based on SEQRES records: (download)

>d2dy4d1 c.55.3.5 (D:1-375) Exonuclease domain of family B DNA polymerases {Bacteriophage RB69 [TaxId: 12353]}
mkefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrk
lfanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirvanfdievtsp
dgfpepsqakhpidaithydsiddrfyvfdllnspygnveewsieiaaklqeqggdevps
eiidkiiympfdnekellmeylnfwqqktpviltgwnvesfaipyvynriknifgestak
rlsphrktrvkvienmygsreiitlfgisvldyidlykkfsftnqpsysldyisefelnv
gklkydgpisklresnhqryisyniiavyrvlqidakrqfinlsldmgyyakiqiqsvfs
piktwdaiifnslke

Sequence, based on observed residues (ATOM records): (download)

>d2dy4d1 c.55.3.5 (D:1-375) Exonuclease domain of family B DNA polymerases {Bacteriophage RB69 [TaxId: 12353]}
mkefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrk
lfanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirvanfdievtsp
dgfpepsqakhpidaithydsiddrfyvfdllnspygnveewsieiaaklqeqggdevps
eiidkiiympfdnekellmeylnfwqqktpviltgwnvesfaipyvynriknifgestak
rlsphrktrvkvieiitlfgisvldyidlykkfsftnqpsysldyisefelnvgklkydg
pisklresnhqryisyniiavyrvlqidakrqfinlsldmgyyakiqiqsvfspiktwda
iifnslke

SCOP Domain Coordinates for d2dy4d1:

Click to download the PDB-style file with coordinates for d2dy4d1.
(The format of our PDB-style files is described here.)

Timeline for d2dy4d1: