SCOPe 2.04: Domain d3rmdd1: 3rmd D:1-375

Lineage for d3rmdd1 (3rmd D:1-375)

1. Root: SCOPe 2.04

2. Class c: Alpha and beta proteins (a/b) [51349] (148 folds)

3. Fold 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. Superfamily c.55.3: Ribonuclease H-like [53098] (15 families)
   consists of one domain of this fold

5. Family c.55.3.5: DnaQ-like 3'-5' exonuclease [53118] (16 proteins)
   contains Pfam PF00929

6. Protein Exonuclease domain of family B DNA polymerases [53125] (8 species)
   elaborated with additional structures and the N-terminal subdomain

7. Species Bacteriophage RB69 [TaxId:12353] [53127] (92 PDB entries)
   additional N-terminal subdomain contains rudimental OB-fold and rudimental ferredoxin-like fold

8. Domain d3rmdd1: 3rmd D:1-375 [249170]
   Other proteins in same PDB: d3rmda2, d3rmdb2, d3rmdc2, d3rmdd2
   automated match to d3l8bb1
   protein/DNA complex; complexed with dtp

Details for d3rmdd1

PDB Entry: 3rmd, 2.98 Å

PDB Description: crystal structure of a replicative dna polymerase bound to dna containing thymine glycol

PDB Compounds: (D:) DNA polymerase

SCOPe Domain Sequences for d3rmdd1:

Sequence; same for both SEQRES and ATOM records:

>d3rmdd1 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

Timeline for d3rmdd1:

• d3rmdd1 is new in SCOPe 2.04-stable
  
• d3rmdd1 appears in SCOPe 2.05
  
• d3rmdd1 appears in the current release, SCOPe 2.08