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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

8YDD

Crystal structure of Nanog(R100A) in complex with Wdr5

Functional Information from GO Data
ChainGOidnamespacecontents
A0000122biological_processnegative regulation of transcription by RNA polymerase II
A0000123cellular_componenthistone acetyltransferase complex
A0001501biological_processskeletal system development
A0005515molecular_functionprotein binding
A0005634cellular_componentnucleus
A0005654cellular_componentnucleoplasm
A0006094biological_processgluconeogenesis
A0006325biological_processchromatin organization
A0006355biological_processregulation of DNA-templated transcription
A0006357biological_processregulation of transcription by RNA polymerase II
A0035097cellular_componenthistone methyltransferase complex
A0042393molecular_functionhistone binding
A0042800molecular_functionhistone H3K4 methyltransferase activity
A0044545cellular_componentNSL complex
A0044665cellular_componentMLL1/2 complex
A0044666cellular_componentMLL3/4 complex
A0045722biological_processpositive regulation of gluconeogenesis
A0045815biological_processtranscription initiation-coupled chromatin remodeling
A0045893biological_processpositive regulation of DNA-templated transcription
A0045995biological_processregulation of embryonic development
A0048188cellular_componentSet1C/COMPASS complex
A0051302biological_processregulation of cell division
A0051726biological_processregulation of cell cycle
A0071339cellular_componentMLL1 complex
A0072686cellular_componentmitotic spindle
A0140004molecular_functionhistone H3Q5ser reader activity
A0140109molecular_functionhistone H3K4me1 reader activity
A0140672cellular_componentATAC complex
B0000122biological_processnegative regulation of transcription by RNA polymerase II
B0000123cellular_componenthistone acetyltransferase complex
B0001501biological_processskeletal system development
B0005515molecular_functionprotein binding
B0005634cellular_componentnucleus
B0005654cellular_componentnucleoplasm
B0006094biological_processgluconeogenesis
B0006325biological_processchromatin organization
B0006355biological_processregulation of DNA-templated transcription
B0006357biological_processregulation of transcription by RNA polymerase II
B0035097cellular_componenthistone methyltransferase complex
B0042393molecular_functionhistone binding
B0042800molecular_functionhistone H3K4 methyltransferase activity
B0044545cellular_componentNSL complex
B0044665cellular_componentMLL1/2 complex
B0044666cellular_componentMLL3/4 complex
B0045722biological_processpositive regulation of gluconeogenesis
B0045815biological_processtranscription initiation-coupled chromatin remodeling
B0045893biological_processpositive regulation of DNA-templated transcription
B0045995biological_processregulation of embryonic development
B0048188cellular_componentSet1C/COMPASS complex
B0051302biological_processregulation of cell division
B0051726biological_processregulation of cell cycle
B0071339cellular_componentMLL1 complex
B0072686cellular_componentmitotic spindle
B0140004molecular_functionhistone H3Q5ser reader activity
B0140109molecular_functionhistone H3K4me1 reader activity
B0140672cellular_componentATAC complex
C0000122biological_processnegative regulation of transcription by RNA polymerase II
C0000123cellular_componenthistone acetyltransferase complex
C0001501biological_processskeletal system development
C0005515molecular_functionprotein binding
C0005634cellular_componentnucleus
C0005654cellular_componentnucleoplasm
C0006094biological_processgluconeogenesis
C0006325biological_processchromatin organization
C0006355biological_processregulation of DNA-templated transcription
C0006357biological_processregulation of transcription by RNA polymerase II
C0035097cellular_componenthistone methyltransferase complex
C0042393molecular_functionhistone binding
C0042800molecular_functionhistone H3K4 methyltransferase activity
C0044545cellular_componentNSL complex
C0044665cellular_componentMLL1/2 complex
C0044666cellular_componentMLL3/4 complex
C0045722biological_processpositive regulation of gluconeogenesis
C0045815biological_processtranscription initiation-coupled chromatin remodeling
C0045893biological_processpositive regulation of DNA-templated transcription
C0045995biological_processregulation of embryonic development
C0048188cellular_componentSet1C/COMPASS complex
C0051302biological_processregulation of cell division
C0051726biological_processregulation of cell cycle
C0071339cellular_componentMLL1 complex
C0072686cellular_componentmitotic spindle
C0140004molecular_functionhistone H3Q5ser reader activity
C0140109molecular_functionhistone H3K4me1 reader activity
C0140672cellular_componentATAC complex
Functional Information from PROSITE/UniProt
site_idPS00027
Number of Residues24
DetailsHOMEOBOX_1 'Homeobox' domain signature. LSsiLnLSykQVKTWFqNqrmkcK
ChainResidueDetails
DLEU129-LYS152
site_idPS00678
Number of Residues15
DetailsWD_REPEATS_1 Trp-Asp (WD) repeats signature. LVSAsdDkTLKIWDV
ChainResidueDetails
ALEU102-VAL116
AILE144-VAL158
AILE186-THR200
AILE274-LEU288
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues117
DetailsRepeat: {"description":"WD 1"}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues123
DetailsRepeat: {"description":"WD 2"}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues120
DetailsRepeat: {"description":"WD 3"}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues117
DetailsRepeat: {"description":"WD 4"}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues82
DetailsRepeat: {"description":"WD 5"}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues120
DetailsRepeat: {"description":"WD 6"}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues102
DetailsRepeat: {"description":"WD 7"}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues12
DetailsSite: {"description":"Important for interaction with histone H3","evidences":[{"evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues3
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"P61964","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues6
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)","evidences":[{"source":"UniProtKB","id":"P61964","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI11
Number of Residues58
DetailsRegion: {"description":"Required for DNA-binding","evidences":[{"source":"UniProtKB","id":"Q9H9S0","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI12
Number of Residues59
DetailsDNA binding: {"description":"Homeobox","evidences":[{"source":"PROSITE-ProRule","id":"PRU00108","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI13
Number of Residues59
DetailsRegion: {"description":"Sufficient for interaction with SALL4","evidences":[{"source":"PubMed","id":"16840789","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

238895

PDB entries from 2025-07-16

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