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 7U0G | pdb_00007u0g

structure of LIN28b nucleosome bound 3 OCT4


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyCore histone-like 8039340 3001387 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyCore histone-like 8039340 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 8099192 3001387 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyCore histone-like 8099192 3001387 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyCore histone-like 8066283 3001387 SCOP2B (2022-06-29)
HSCOP2B SuperfamilyCore histone-like 8066283 3001387 SCOP2B (2022-06-29)
KSCOP2B Superfamilylambda C1 repressor DNA-binding domain-like 8094725 3000119 SCOP2B (2022-06-29)
LSCOP2B Superfamilylambda C1 repressor DNA-binding domain-like 8094725 3000119 SCOP2B (2022-06-29)
MSCOP2B Superfamilylambda C1 repressor DNA-binding domain-like 8094725 3000119 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
AAsparaginase_2e7u0gA1 A: alpha arraysX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Asparaginase_2ECOD (v295.2)
Ezf-AN1e7u0gE1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: FMN-binding split barrelF: zf-AN1ECOD (v295.2)
Bzf-AN1e7u0gB1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: FMN-binding split barrelF: zf-AN1ECOD (v295.2)
FAsparaginase_2e7u0gF1 A: alpha arraysX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Asparaginase_2ECOD (v295.2)
CAsparaginase_2e7u0gC1 A: alpha arraysX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Asparaginase_2ECOD (v295.2)
Gzf-AN1e7u0gG1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: FMN-binding split barrelF: zf-AN1ECOD (v295.2)
Dzf-AN1e7u0gD1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: FMN-binding split barrelF: zf-AN1ECOD (v295.2)
HAsparaginase_2e7u0gH1 A: alpha arraysX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Asparaginase_2ECOD (v295.2)
Kzf-AN1e7u0gK1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: FMN-binding split barrelF: zf-AN1ECOD (v295.2)
LAsparaginase_2e7u0gL1 A: alpha arraysX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Asparaginase_2ECOD (v295.2)
MAsparaginase_2e7u0gM1 A: alpha arraysX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Asparaginase_2ECOD (v295.2)
Nzf-AN1e7u0gN1 A: alpha arraysX: cradle loop barrelH: RIFT-relatedT: FMN-binding split barrelF: zf-AN1ECOD (v295.2)
OAsparaginase_2e7u0gO1 A: alpha arraysX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Asparaginase_2ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
N2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (utative)
O2.60.40.10 Mainly Beta Sandwich Immunoglobulin-like ImmunoglobulinsCATH (utative)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, E
PF00125Core histone H2A/H2B/H3/H4 domain (Histone)Core histone H2A/H2B/H3/H4 domainDomain
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 ...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
C, G
PF16211C-terminus of histone H2A (Histone_H2A_C)C-terminus of histone H2A- Family
K, L, M
PF00046Homeodomain (Homeodomain)HomeodomainDomain
K, L, M
PF00157Pou domain - N-terminal to homeobox domain (Pou)Pou domain - N-terminal to homeobox domainDomain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, E
Histone H3.1
B, F
Histone H4
C, G
Histone H2A type 2-C
D, H
Histone H2B type 2-E
DNA (162-MER)---
DNA (162-MER)---
K, L, M
Maltodextrin-binding protein,POU domain, class 5, transcription factor 1
N, O
Single-chain variable fragment---

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, E
IPR009072Histone-foldHomologous Superfamily
A, E
IPR007125Core Histone H2A/H2B/H3 domainDomain
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
IPR002119Histone H2AFamily
C, G
IPR007125Core Histone H2A/H2B/H3 domainDomain
C, G
IPR061508Histone H2A, histone foldDomain
C, G
IPR032454Histone H2A, C-terminal domainDomain
C, G
IPR032458Histone H2A conserved siteConserved Site
D, H
IPR009072Histone-foldHomologous Superfamily
D, H
IPR000558Histone H2BFamily
D, H
IPR007125Core Histone H2A/H2B/H3 domainDomain
D, H
IPR055333Histone H2B, conserved siteConserved Site
K, L, M
IPR006061Solute-binding family 1, conserved siteConserved Site
K, L, M
IPR006060Maltose/Cyclodextrin ABC transporter, substrate-binding proteinFamily
K, L, M
IPR006059Bacterial-type extracellular solute-binding proteinFamily
K, L, M
IPR009057Homeodomain-like superfamilyHomologous Superfamily
K, L, M
IPR000327POU-specific domainDomain
K, L, M
IPR013847POU domainDomain
K, L, M
IPR017970Homeobox, conserved siteConserved Site
K, L, M
IPR050255POU domain transcription factorFamily
K, L, M
IPR010982Lambda repressor-like, DNA-binding domain superfamilyHomologous Superfamily
K, L, M
IPR001356HomeodomainDomain

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
A, E
:  P68431
B, F
:  P62805
C, G
:  Q16777
D, H
:  Q16778
K, L, M
:  Q01860