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 8VWT | pdb_00008vwt

OGG1 bound to a nucleosome containing 8oxoG at SHL-6 (composite map)


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
KSCOP2B SuperfamilyDNA-glycosylase 8036319 3000905 SCOP2B (2022-06-29)
KSCOP2B SuperfamilyTATA-box binding protein-like 8036320 3000705 SCOP2B (2022-06-29)
H [auth D]SCOP2B SuperfamilyCore histone-like 8066267 3001387 SCOP2B (2022-06-29)
D [auth H]SCOP2B SuperfamilyCore histone-like 8066267 3001387 SCOP2B (2022-06-29)
G [auth C]SCOP2B SuperfamilyCore histone-like 8067130 3001387 SCOP2B (2022-06-29)
C [auth G]SCOP2B SuperfamilyCore histone-like 8067130 3001387 SCOP2B (2022-06-29)
F [auth B]SCOP2B SuperfamilyCore histone-like 8070545 3001387 SCOP2B (2022-06-29)
B [auth F]SCOP2B SuperfamilyCore histone-like 8070545 3001387 SCOP2B (2022-06-29)
E [auth A]SCOP2B SuperfamilyCore histone-like 8070531 3001387 SCOP2B (2022-06-29)
A [auth E]SCOP2B SuperfamilyCore histone-like 8070531 3001387 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
Ke8vwtK01 A: alpha arraysX: Hypothetical protein YqbG-likeH: Hypothetical protein YqbG-likeT: alpha/beta-HydrolasesF:ECOD (v295.2)
H [auth D]V-sete8vwtD1 A: alpha arraysX: Hypothetical protein YqbG-likeH: Hypothetical protein YqbG-likeT: alpha/beta-HydrolasesF: V-setECOD (v295.2)
D [auth H]V-sete8vwtH1 A: alpha arraysX: Hypothetical protein YqbG-likeH: Hypothetical protein YqbG-likeT: alpha/beta-HydrolasesF: V-setECOD (v295.2)
G [auth C]V-sete8vwtC1 A: alpha arraysX: Hypothetical protein YqbG-likeH: Hypothetical protein YqbG-likeT: alpha/beta-HydrolasesF: V-setECOD (v295.2)
C [auth G]V-sete8vwtG1 A: alpha arraysX: Hypothetical protein YqbG-likeH: Hypothetical protein YqbG-likeT: alpha/beta-HydrolasesF: V-setECOD (v295.2)
F [auth B]V-sete8vwtB1 A: alpha arraysX: Hypothetical protein YqbG-likeH: Hypothetical protein YqbG-likeT: alpha/beta-HydrolasesF: V-setECOD (v295.2)
B [auth F]V-sete8vwtF1 A: alpha arraysX: Hypothetical protein YqbG-likeH: Hypothetical protein YqbG-likeT: alpha/beta-HydrolasesF: V-setECOD (v295.2)
E [auth A]V-sete8vwtA1 A: alpha arraysX: Hypothetical protein YqbG-likeH: Hypothetical protein YqbG-likeT: alpha/beta-HydrolasesF: V-setECOD (v295.2)
A [auth E]V-sete8vwtE1 A: alpha arraysX: Hypothetical protein YqbG-likeH: Hypothetical protein YqbG-likeT: alpha/beta-HydrolasesF: V-setECOD (v295.2)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF079348-oxoguanine DNA glycosylase, N-terminal domain (OGG_N)8-oxoguanine DNA glycosylase, N-terminal domain- Family
PF00730HhH-GPD superfamily base excision DNA repair protein (HhH-GPD)HhH-GPD superfamily base excision DNA repair proteinThis family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate [2]. This includes endonucle ...This family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate [2]. This includes endonuclease III, EC:4.2.99.18 and MutY an A/G-specific adenine glycosylase, both have a C terminal 4Fe-4S cluster. The family also includes 8-oxoguanine DNA glycosylases such as Swiss:P53397. The methyl-CPG binding protein MBD4 Swiss:Q9Z2D7 also contains a related domain [1] that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other members of the AlkA family.
Domain
C [auth G],
G [auth C]
PF16211C-terminus of histone H2A (Histone_H2A_C)C-terminus of histone H2A- Family
B [auth F],
F [auth B]
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 ...CENP-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 associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure. The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes. This domain is the C-terminal histone fold domain of CENP-T, which associates with chromatin [2-3].
Domain
A [auth E],
E [auth A]
PF00125Core histone H2A/H2B/H3/H4 domain (Histone)Core histone H2A/H2B/H3/H4 domainDomain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
N-glycosylase/DNA lyase
601 J strand (damaged strand)---
601 I strand (non-damaged strand)---
D [auth H],
H [auth D]
Histone H2B type 1-C/E/F/G/I
C [auth G],
G [auth C]
Histone H2A type 1
B [auth F],
F [auth B]
Histone H4
A [auth E],
E [auth A]
Histone H3.2

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR003265HhH-GPD domainDomain
IPR023170Helix-hairpin-helix, base-excision DNA repair, C-terminalHomologous Superfamily
IPR011257DNA glycosylaseHomologous Superfamily
IPR052054Oxidative DNA damage repair enzymeFamily
IPR0129048-oxoguanine DNA glycosylase, N-terminalDomain
IPR0045778-oxoguanine DNA-glycosylaseFamily
D [auth H],
H [auth D]
IPR009072Histone-foldHomologous Superfamily
D [auth H],
H [auth D]
IPR000558Histone H2BFamily
D [auth H],
H [auth D]
IPR007125Core Histone H2A/H2B/H3 domainDomain
D [auth H],
H [auth D]
IPR055333Histone H2B, conserved siteConserved Site
C [auth G],
G [auth C]
IPR009072Histone-foldHomologous Superfamily
C [auth G],
G [auth C]
IPR002119Histone H2AFamily
C [auth G],
G [auth C]
IPR007125Core Histone H2A/H2B/H3 domainDomain
C [auth G],
G [auth C]
IPR061508Histone H2A, histone foldDomain
C [auth G],
G [auth C]
IPR032454Histone H2A, C-terminal domainDomain
C [auth G],
G [auth C]
IPR032458Histone H2A conserved siteConserved Site
B [auth F],
F [auth B]
IPR009072Histone-foldHomologous Superfamily
B [auth F],
F [auth B]
IPR035425CENP-T/Histone H4, histone foldDomain
B [auth F],
F [auth B]
IPR001951Histone H4Family
B [auth F],
F [auth B]
IPR019809Histone H4, conserved siteConserved Site
B [auth F],
F [auth B]
IPR004823TATA box binding protein associated factor (TAF), histone-like fold domainDomain
A [auth E],
E [auth A]
IPR009072Histone-foldHomologous Superfamily
A [auth E],
E [auth A]
IPR007125Core Histone H2A/H2B/H3 domainDomain
A [auth E],
E [auth A]
IPR000164Histone H3/CENP-AFamily

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
:  O15527
D [auth H],
H [auth D]
:  P62807
C [auth G],
G [auth C]
:  P0C0S8
B [auth F],
F [auth B]
:  P62805
A [auth E],
E [auth A]
:  Q71DI3