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4GM8

Crystal structure of human WD repeat domain 5 with compound MM-102

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
A0035064molecular_functionmethylated histone binding
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
A0090043biological_processregulation of tubulin deacetylation
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
B0035064molecular_functionmethylated histone binding
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
B0090043biological_processregulation of tubulin deacetylation
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
C0035064molecular_functionmethylated histone binding
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
C0090043biological_processregulation of tubulin deacetylation
C0140672cellular_componentATAC complex
D0000122biological_processnegative regulation of transcription by RNA polymerase II
D0000123cellular_componenthistone acetyltransferase complex
D0001501biological_processskeletal system development
D0005515molecular_functionprotein binding
D0005634cellular_componentnucleus
D0005654cellular_componentnucleoplasm
D0006094biological_processgluconeogenesis
D0006325biological_processchromatin organization
D0006355biological_processregulation of DNA-templated transcription
D0006357biological_processregulation of transcription by RNA polymerase II
D0035064molecular_functionmethylated histone binding
D0035097cellular_componenthistone methyltransferase complex
D0042393molecular_functionhistone binding
D0042800molecular_functionhistone H3K4 methyltransferase activity
D0044545cellular_componentNSL complex
D0044665cellular_componentMLL1/2 complex
D0044666cellular_componentMLL3/4 complex
D0045722biological_processpositive regulation of gluconeogenesis
D0045815biological_processtranscription initiation-coupled chromatin remodeling
D0045893biological_processpositive regulation of DNA-templated transcription
D0045995biological_processregulation of embryonic development
D0048188cellular_componentSet1C/COMPASS complex
D0051302biological_processregulation of cell division
D0051726biological_processregulation of cell cycle
D0071339cellular_componentMLL1 complex
D0072686cellular_componentmitotic spindle
D0090043biological_processregulation of tubulin deacetylation
D0140672cellular_componentATAC complex
Functional Information from PDB Data
site_idAC1
Number of Residues17
DetailsBINDING SITE FOR CHAIN E OF MM-102
ChainResidue
AGLY89
APHE263
ALEU321
AHOH428
DTYR131
EHOH101
EHOH102
H0XL2
H0XN5
AILE90
ASER91
AASP107
ATYR131
APHE133
APHE149
ATYR260
ACYS261

site_idAC2
Number of Residues20
DetailsBINDING SITE FOR CHAIN F OF MM-102
ChainResidue
BSER49
BGLY89
BILE90
BSER91
BASP107
BTYR131
BPHE133
BPHE149
BLYS259
BTYR260
BCYS261
BPHE263
BLEU321
BHOH434
BHOH451
BHOH473
CTYR131
FHOH101
G0XL2
G0XN5

site_idAC3
Number of Residues18
DetailsBINDING SITE FOR CHAIN G OF MM-102
ChainResidue
BTYR131
CSER49
CGLY89
CILE90
CSER91
CASP107
CTYR131
CPHE133
CPHE149
CTYR260
CCYS261
CPHE263
CLEU321
CHOH472
F0XL2
F0XN5
GHOH101
GHOH102

site_idAC4
Number of Residues17
DetailsBINDING SITE FOR CHAIN H OF MM-102
ChainResidue
ATYR131
DGLY89
DILE90
DSER91
DASP107
DPHE133
DPHE149
DLYS259
DTYR260
DCYS261
DPHE263
DILE305
DLEU321
DHOH468
E0XL2
E0XN5
HHOH101

Functional Information from PROSITE/UniProt
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 Residues16
DetailsSITE: Important for interaction with histone H3
ChainResidueDetails
AASP107
CPHE133
CPHE263
CGLU322
DASP107
DPHE133
DPHE263
DGLU322
APHE133
APHE263
AGLU322
BASP107
BPHE133
BPHE263
BGLU322
CASP107

site_idSWS_FT_FI2
Number of Residues4
DetailsMOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861
ChainResidueDetails
ALYS112
BLYS112
CLYS112
DLYS112

site_idSWS_FT_FI3
Number of Residues12
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:28112733
ChainResidueDetails
ALYS27
DLYS27
DLYS46
ALYS46
BLYS27
BLYS46
CLYS27
CLYS46

222415

PDB entries from 2024-07-10

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