Lineage for d2p5od1 (2p5o D:1-375)

  1. Root: SCOPe 2.06
  2. 2078559Class c: Alpha and beta proteins (a/b) [51349] (148 folds)
  3. 2122050Fold 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. 2123751Superfamily c.55.3: Ribonuclease H-like [53098] (15 families) (S)
    consists of one domain of this fold
  5. 2124334Family c.55.3.5: DnaQ-like 3'-5' exonuclease [53118] (17 protein domains)
    contains Pfam PF00929
  6. 2124346Protein Exonuclease domain of family B DNA polymerases [53125] (8 species)
    elaborated with additional structures and the N-terminal subdomain
  7. 2124347Species Bacteriophage RB69 [TaxId:12353] [53127] (92 PDB entries)
    additional N-terminal subdomain contains rudimental OB-fold and rudimental ferredoxin-like fold
  8. 2124477Domain d2p5od1: 2p5o D:1-375 [139504]
    Other proteins in same PDB: d2p5oa2, d2p5ob2, d2p5oc2, d2p5od2
    automatically matched to d1clqa1
    protein/DNA complex

Details for d2p5od1

PDB Entry: 2p5o (more details), 2.8 Å

PDB Description: Crystal structure of RB69 GP43 in complex with DNA containing an abasic site analog
PDB Compounds: (D:) DNA polymerase

SCOPe Domain Sequences for d2p5od1:

Sequence, based on SEQRES records: (download)

>d2p5od1 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)

>d2p5od1 c.55.3.5 (D:1-375) Exonuclease domain of family B DNA polymerases {Bacteriophage RB69 [TaxId: 12353]}
mkefyltveqigdsiferyidsngrertreveykpslfahcpesqatkyfdiygkpctrk
lfanmrdasqwikrmediglealgmddfklaylsdtynyeikydhtkirfdnekellmey
lnfwqqktpviltgwnvesfaipyvynriknifgestakrlsphrktrvkveiitlfgis
vldyidlykkfsftnqpsysldyisefelnvgklkydgpisklresnhqryisyniiavy
rvlqidakrqfinlsldmgyyakiqiqsvfspiktwdaiifnslke

SCOPe Domain Coordinates for d2p5od1:

Click to download the PDB-style file with coordinates for d2p5od1.
(The format of our PDB-style files is described here.)

Timeline for d2p5od1: