9DWI | pdb_00009dwi

DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 3, composite)


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyCore histone-like 8070531 3001387 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyCore histone-like 8070531 3001387 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyCore histone-like 8070545 3001387 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyCore histone-like 8070545 3001387 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyCore histone-like 8067130 3001387 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyCore histone-like 8067130 3001387 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyCore histone-like 8066267 3001387 SCOP2B (2022-06-29)
HSCOP2B SuperfamilyCore histone-like 8066267 3001387 SCOP2B (2022-06-29)
LSCOP2B SuperfamilyNucleotidyltransferase-like 8041162 3000129 SCOP2B (2022-06-29)
LSCOP2B SuperfamilyPsbU/PolX domain-like 8041160 3000893 SCOP2B (2022-06-29)
LSCOP2B SuperfamilyDNA polymerase beta, N-terminal domain-like 8041159 3000524 SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
B, F
PF15511Centromere kinetochore component CENP-T histone fold (CENP-T_C)Centromere kinetochore component CENP-T histone foldCENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly asso ...Domain
C, G
PF16211C-terminus of histone H2A (Histone_H2A_C)C-terminus of histone H2A- Family
PF14716Helix-hairpin-helix domain (HHH_8)Helix-hairpin-helix domainDomain
PF14791DNA polymerase beta thumb (DNA_pol_B_thumb)DNA polymerase beta thumb- Family
PF14792DNA polymerase beta palm (DNA_pol_B_palm)DNA polymerase beta palmThe catalytic region of DNA polymerase beta is split into three domains. An N-terminal fingers domain, a central palm domain and a C-terminal thumb domain. This entry represents the palm domain [1]. Domain
PF10391Fingers domain of DNA polymerase lambda (DNA_pol_lambd_f)Fingers domain of DNA polymerase lambdaDNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. DNA_pol_lambd_f is the centr ...Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, E
Histone H3.2
B, F
Histone H4
C, G
Histone H2A type 1
D, H
Histone H2B type 1-C/E/F/G/I
601 I strand (damaged strand 1)---
601 J strand (non-damaged strand)---
601 K strand (damaged strand 2)---
DNA polymerase beta

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, E
IPR009072Histone-foldHomologous Superfamily
A, E
IPR007125Histone H2A/H2B/H3Domain
A, E
IPR000164Histone H3/CENP-AFamily
B, F
IPR009072Histone-foldHomologous Superfamily
B, F
IPR035425CENP-T/Histone H4, histone foldDomain
B, F
IPR001951Histone H4Family
B, F
IPR019809Histone H4, conserved siteConserved Site
B, F
IPR004823TATA box binding protein associated factor (TAF), histone-like fold domainDomain
C, G
IPR009072Histone-foldHomologous Superfamily
C, G
IPR007125Histone H2A/H2B/H3Domain
C, G
IPR002119Histone H2AFamily
C, G
IPR032454Histone H2A, C-terminal domainDomain
C, G
IPR032458Histone H2A conserved siteConserved Site
D, H
IPR009072Histone-foldHomologous Superfamily
D, H
IPR007125Histone H2A/H2B/H3Domain
D, H
IPR000558Histone H2BFamily
D, H
IPR055333Histone H2B, conserved siteConserved Site
IPR037160DNA polymerase, thumb domain superfamilyHomologous Superfamily
IPR019843DNA polymerase family X, binding siteBinding Site
IPR029398DNA polymerase beta, thumb domainDomain
IPR002008DNA polymerase family X, beta-likeFamily
IPR043519Nucleotidyltransferase superfamilyHomologous Superfamily
IPR027421DNA polymerase lambda lyase domain superfamilyHomologous Superfamily
IPR003583Helix-hairpin-helix DNA-binding motif, class 1Domain
IPR028207DNA polymerase beta, palm domainDomain
IPR022312DNA polymerase family XFamily
IPR010996DNA polymerase beta-like, N-terminal domainDomain
IPR018944DNA polymerase lambda, fingers domainDomain
IPR002054DNA-directed DNA polymerase XDomain

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
A, E
PharosQ71DI3
B, F
PharosP62805
C, G
PharosP0C0S8
D, H
PharosP62807
PharosP06746