6S1N | pdb_00006s1n

Human polymerase delta holoenzyme Conformer 2


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
BSCOP2B SuperfamilyMetallo-dependent phosphatases 8053383 3001067 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyNucleic acid-binding proteins 8053386 3000135 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyWinged helix DNA-binding domain 8054002 3000034 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyDNA clamp 8032796 3000780 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyDNA clamp 8032799 3000780 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyDNA clamp 8032796 3000780 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyDNA clamp 8032799 3000780 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyDNA clamp 8032796 3000780 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyDNA clamp 8032799 3000780 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
BKOG2732e6s1nB2 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: KOG2732ECOD (1.6)
BDNA_pol_E_Be6s1nB1 A: a+b four layersX: Carbon-nitrogen hydrolase-likeH: Metallo-dependent phosphatases (From Topology)T: Metallo-dependent phosphatasesF: DNA_pol_E_BECOD (1.6)
CCDC27e6s1nC1 A: alpha arraysX: HTHH: HTHT: wingedF: CDC27ECOD (1.6)
EPCNA_Ne6s1nE1 A: a+b two layersX: DNA clamp (From Topology)H: DNA clamp (From Topology)T: DNA clampF: PCNA_NECOD (1.6)
EPCNA_Ce6s1nE2 A: a+b two layersX: DNA clamp (From Topology)H: DNA clamp (From Topology)T: DNA clampF: PCNA_CECOD (1.6)
FPCNA_Ne6s1nF1 A: a+b two layersX: DNA clamp (From Topology)H: DNA clamp (From Topology)T: DNA clampF: PCNA_NECOD (1.6)
FPCNA_Ce6s1nF2 A: a+b two layersX: DNA clamp (From Topology)H: DNA clamp (From Topology)T: DNA clampF: PCNA_CECOD (1.6)
GPCNA_Ne6s1nG1 A: a+b two layersX: DNA clamp (From Topology)H: DNA clamp (From Topology)T: DNA clampF: PCNA_NECOD (1.6)
GPCNA_Ce6s1nG2 A: a+b two layersX: DNA clamp (From Topology)H: DNA clamp (From Topology)T: DNA clampF: PCNA_CECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF14260C4-type zinc-finger of DNA polymerase delta (zf-C4pol)C4-type zinc-finger of DNA polymerase deltaIn fission yeast this zinc-finger domain appears is the region of Pol3 that binds directly to the B-subunit, Cdc1 [1]. Pol delta is a hetero-tetrameric enzyme comprising four evolutionarily well-conserved proteins: the catalytic subunit Pol3 and thr ...Domain
PF00136DNA polymerase family B (DNA_pol_B)DNA polymerase family B- Family
PF03104DNA polymerase family B, exonuclease domain (DNA_pol_B_exo1)DNA polymerase family B, exonuclease domain- Family
PF04042DNA polymerase alpha/epsilon subunit B (DNA_pol_E_B)DNA polymerase alpha/epsilon subunit B- Family
PF18018DNA polymerase delta subunit OB-fold domain (DNA_pol_D_N)DNA polymerase delta subunit OB-fold domainThe eukaryotic DNA polymerase delta (Pol delta) participates in genome replication, homologous recombination, DNA repair and damage tolerance [1]. Human Pol delta consists of four subunits: p125, p50, p66 and p12. The first three subunits correspond ...Domain
PF09507DNA polymerase subunit Cdc27 (CDC27)DNA polymerase subunit Cdc27- Family
E, F, G
PF02747Proliferating cell nuclear antigen, C-terminal domain (PCNA_C)Proliferating cell nuclear antigen, C-terminal domainN-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA. Domain
E, F, G
PF00705Proliferating cell nuclear antigen, N-terminal domain (PCNA_N)Proliferating cell nuclear antigen, N-terminal domainN-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA. Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
DNA polymerase delta catalytic subunit
DNA polymerase delta subunit 2
DNA polymerase delta subunit 3
DNA polymerase delta subunit 4-
E, F, G
Proliferating cell nuclear antigen
H [auth P]DNA primer---
I [auth T]DNA template---

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR036397Ribonuclease H superfamilyHomologous Superfamily
IPR006134DNA-directed DNA polymerase, family B, multifunctional domainDomain
IPR050240DNA polymerase type-BFamily
IPR017964DNA-directed DNA polymerase, family B, conserved siteConserved Site
IPR012337Ribonuclease H-like superfamilyHomologous Superfamily
IPR023211DNA polymerase, palm domain superfamilyHomologous Superfamily
IPR006172DNA-directed DNA polymerase, family BFamily
IPR025687C4-type zinc-finger of DNA polymerase deltaDomain
IPR043502DNA/RNA polymerase superfamilyHomologous Superfamily
IPR006133DNA-directed DNA polymerase, family B, exonuclease domainDomain
IPR042087DNA polymerase family B, thumb domainHomologous Superfamily
IPR024826DNA polymerase delta/II small subunit familyFamily
IPR007185DNA polymerase alpha/delta/epsilon, subunit BDomain
IPR040663DNA polymerase delta subunit, OB-fold domainDomain
IPR041863DNA polymerase delta subunit 2, C-terminal domainDomain
IPR019038DNA polymerase delta subunit 3Family
IPR041913DNA polymerase delta subunit 3 superfamilyHomologous Superfamily
IPR007218DNA polymerase delta, subunit 4Family
E, F, G
IPR046938DNA clamp superfamilyHomologous Superfamily
E, F, G
IPR022648Proliferating cell nuclear antigen, PCNA, N-terminalDomain
E, F, G
IPR000730Proliferating cell nuclear antigen, PCNAFamily
E, F, G
IPR022649Proliferating cell nuclear antigen, PCNA, C-terminalDomain
E, F, G
IPR022659Proliferating cell nuclear antigen, PCNA, conserved siteConserved Site

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
PharosP28340
PharosP49005
PharosQ15054
E, F, G
PharosP12004