3PDN

Crystal structure of SmyD3 in complex with methyltransferase inhibitor sinefungin

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000978	molecular_function	RNA polymerase II cis-regulatory region sequence-specific DNA binding
A	0000993	molecular_function	RNA polymerase II complex binding
A	0001162	molecular_function	RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005737	cellular_component	cytoplasm
A	0006325	biological_process	chromatin organization
A	0006338	biological_process	chromatin remodeling
A	0007507	biological_process	heart development
A	0008168	molecular_function	methyltransferase activity
A	0008270	molecular_function	zinc ion binding
A	0016740	molecular_function	transferase activity
A	0032259	biological_process	methylation
A	0042054	molecular_function	histone methyltransferase activity
A	0045892	biological_process	negative regulation of DNA-templated transcription
A	0046872	molecular_function	metal ion binding
A	0140939	molecular_function	histone H4 methyltransferase activity
A	0140954	molecular_function	histone H3K36 dimethyltransferase activity
A	0140999	molecular_function	histone H3K4 trimethyltransferase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	23
Details	BINDING SITE FOR RESIDUE SFG A 429

Chain	Residue
A	ARG14
A	LEU204
A	ASN205
A	HIS206
A	TYR239
A	TYR257
A	PHE259
A	GOL431
A	HOH655
A	HOH670
A	HOH674
A	ASN16
A	HOH697
A	HOH725
A	HOH766
A	HOH827
A	TYR124
A	GLU130
A	ASN132
A	CYS180
A	ASN181
A	SER202
A	LEU203

---

site_id	AC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL A 430

Chain	Residue
A	CYS238
A	LEU240
A	MET242
A	HIS366
A	GOL432
A	HOH669
A	HOH678
A	HOH837

---

site_id	AC3
Number of Residues	10
Details	BINDING SITE FOR RESIDUE GOL A 431

Chain	Residue
A	ASN181
A	SER182
A	PHE183
A	SER202
A	ILE237
A	TYR239
A	TYR257
A	SFG429
A	HOH702
A	HOH938

---

site_id	AC4
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL A 432

Chain	Residue
A	ILE214
A	VAL215
A	HIS366
A	PRO367
A	VAL368
A	GOL430
A	HOH652
A	HOH693
A	HOH779

---

site_id	AC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL A 433

Chain	Residue
A	PRO81
A	ASP82
A	LYS111
A	GLY115
A	GLU142
A	GLN146
A	HOH536
A	HOH738
A	HOH1015

---

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL A 434

Chain	Residue
A	PHE151
A	GLN152
A	ILE159
A	LEU171
A	HOH602
A	HOH817

---

site_id	AC7
Number of Residues	11
Details	BINDING SITE FOR RESIDUE GOL A 435

Chain	Residue
A	PHE126
A	ALA168
A	PHE169
A	ASP170
A	GLU173
A	ALA174
A	LYS177
A	HOH461
A	HOH528
A	HOH853
A	HOH1036

---

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 436

Chain	Residue
A	CYS62
A	CYS65
A	HIS83
A	CYS87

---

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 437

Chain	Residue
A	CYS49
A	CYS52
A	CYS71
A	CYS75

---

site_id	BC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 438

Chain	Residue
A	CYS208
A	CYS261
A	CYS263
A	CYS266

---

site_id	BC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG A 439

Chain	Residue
A	HOH751
A	HOH791
A	HOH875
A	HOH932
A	HOH1002
A	HOH1003

---

site_id	BC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG A 440

Chain	Residue
A	HOH869
A	HOH896
A	HOH1004
A	HOH1005
A	HOH1006

---

Functional Information from PROSITE/UniProt

site_id	PS01360
Number of Residues	39
Details	ZF_MYND_1 Zinc finger MYND-type signature. Cdr..Cllgkeklmr........CsqCrvakYCsakCqkkawpd..Hkre.C

Chain	Residue	Details
A	CYS49-CYS87

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	236
Details	Domain: {"description":"SET","evidences":[{"source":"PROSITE-ProRule","id":"PRU00190","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	38
Details	Zinc finger: {"description":"MYND-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00134","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	156
Details	Region: {"description":"C-terminal domain; essential for histone methyltransferase activity, nuclear localization and mediates interaction with HSP90AA1","evidences":[{"source":"PubMed","id":"25738358","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"APR-2010","submissionDatabase":"PDB data bank","title":"Crystal structure of human histone-lysine n-methyltransferase SMYD3 in complex with S-adenosyl-L-methionine.","authoringGroup":["Structural genomics consortium (SGC)"]}}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00134","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	5
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00190","evidenceCode":"ECO:0000255"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"APR-2010","submissionDatabase":"PDB data bank","title":"Crystal structure of human histone-lysine n-methyltransferase SMYD3 in complex with S-adenosyl-L-methionine.","authoringGroup":["Structural genomics consortium (SGC)"]}}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	1
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

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