Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6WHZ

Histone deacetylases complex with peptide macrocycles

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004407	molecular_function	histone deacetylase activity
B	0004407	molecular_function	histone deacetylase activity
C	0004407	molecular_function	histone deacetylase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	binding site for residue ZN A 401

Chain	Residue
A	ASP181
A	HIS183
A	ASP269
D	U2M500

site_id	AC2
Number of Residues	5
Details	binding site for residue NA A 402

Chain	Residue
A	ASP179
A	ASP181
A	HIS183
A	SER202
A	PHE203

site_id	AC3
Number of Residues	4
Details	binding site for residue NA A 403

Chain	Residue
A	PHE192
A	THR195
A	VAL198
A	TYR227

site_id	AC4
Number of Residues	4
Details	binding site for residue PGE A 405

Chain	Residue
A	ASP23
A	ASN26
A	ASP109
B	GLN133

site_id	AC5
Number of Residues	4
Details	binding site for residue ZN B 401

Chain	Residue
B	ASP181
B	HIS183
B	ASP269
F	U2M500

site_id	AC6
Number of Residues	6
Details	binding site for residue NA B 402

Chain	Residue
B	ASP179
B	ASP181
B	HIS183
B	SER202
B	PHE203
B	HIS204

site_id	AC7
Number of Residues	4
Details	binding site for residue NA B 403

Chain	Residue
B	PHE192
B	THR195
B	VAL198
B	TYR227

site_id	AC8
Number of Residues	1
Details	binding site for residue PG4 B 404

Chain	Residue
B	ASN26

site_id	AC9
Number of Residues	3
Details	binding site for residue PGE B 405

Chain	Residue
B	GLU340
B	TYR341
B	GLY343

site_id	AD1
Number of Residues	5
Details	binding site for residue ZN C 401

Chain	Residue
C	ASP181
C	HIS183
C	ASP269
C	TYR308
G	U2M500

site_id	AD2
Number of Residues	6
Details	binding site for residue NA C 402

Chain	Residue
C	ASP179
C	ASP181
C	HIS183
C	SER202
C	PHE203
C	HIS204

site_id	AD3
Number of Residues	3
Details	binding site for residue PGE C 403

Chain	Residue
C	ALA191
C	PHE192
C	ARG197

site_id	AD4
Number of Residues	4
Details	binding site for Ligand residues HYP D 502 through LYS D 503 bound to ASN D 501

Chain	Residue
D	U2M500
D	ASN501
D	GLN504
D	HOH601

site_id	AD5
Number of Residues	3
Details	binding site for Ligand residues HYP F 502 through LYS F 503 bound to ASN F 501

Chain	Residue
F	U2M500
F	ASN501
F	GLN504

site_id	AD6
Number of Residues	7
Details	binding site for Ligand residues HYP G 502 through LYS G 503 bound to ASN G 501

Chain	Residue
C	LEU276
C	LEU378
G	U2M500
G	ASN501
G	GLN504
G	DLY505
G	HOH601

site_id	AD7
Number of Residues	12
Details	binding site for Di-peptide U2M D 500 and GLY D 507

Chain	Residue
A	ASP104
A	HIS145
A	HIS146
A	GLY154
A	PHE155
A	HIS183
A	PHE210
A	TYR308
A	ZN401
D	ASN501
D	HYP502
D	TRP506

site_id	AD8
Number of Residues	12
Details	binding site for Di-peptide U2M D 500 and ASN D 501

Chain	Residue
A	ASP104
A	HIS145
A	HIS146
A	GLY154
A	PHE155
A	HIS183
A	TYR308
A	ZN401
D	HYP502
D	LYS503
D	GLN504
D	GLY507

site_id	AD9
Number of Residues	7
Details	binding site for Di-peptide GLN D 504 and DLY D 505

Chain	Residue
A	GLU103
A	ASN297
A	HOH502
D	ASN501
D	HYP502
D	LYS503
D	TRP506

site_id	AE1
Number of Residues	8
Details	binding site for Di-peptide DLY D 505 and TRP D 506

Chain	Residue
A	HOH502
D	GLN504
D	GLY507
A	LYS13
A	LYS15
A	GLU103
A	ASP135
A	ASN297

site_id	AE2
Number of Residues	12
Details	binding site for Di-peptide U2M F 500 and GLY F 507

Chain	Residue
B	ASP104
B	HIS146
B	GLY154
B	PHE155
B	HIS183
B	PHE210
B	TYR308
B	ZN401
F	ASN501
F	HYP502
F	DLY505
F	TRP506

site_id	AE3
Number of Residues	13
Details	binding site for Di-peptide U2M F 500 and ASN F 501

Chain	Residue
B	ASP104
B	HIS146
B	GLY154
B	PHE155
B	HIS183
B	PHE210
B	LEU276
B	TYR308
B	ZN401
F	HYP502
F	LYS503
F	GLN504
F	GLY507

site_id	AE4
Number of Residues	6
Details	binding site for Di-peptide GLN F 504 and DLY F 505

Chain	Residue
B	ASP104
F	ASN501
F	HYP502
F	LYS503
F	TRP506
F	GLY507

site_id	AE5
Number of Residues	3
Details	binding site for Di-peptide DLY F 505 and TRP F 506

Chain	Residue
B	ASP104
F	GLN504
F	GLY507

site_id	AE6
Number of Residues	14
Details	binding site for Di-peptide U2M G 500 and ASN G 501

Chain	Residue
C	ASP104
C	HIS146
C	GLY154
C	PHE155
C	HIS183
C	PHE210
C	LEU276
C	TYR308
C	ZN401
G	HYP502
G	LYS503
G	GLN504
G	TRP506
G	GLY507

site_id	AE7
Number of Residues	13
Details	binding site for Di-peptide U2M G 500 and GLY G 507

Chain	Residue
C	ASP104
C	HIS146
C	GLY154
C	PHE155
C	HIS183
C	PHE210
C	LEU276
C	TYR308
C	ZN401
G	ASN501
G	HYP502
G	DLY505
G	TRP506

site_id	AE8
Number of Residues	7
Details	binding site for Di-peptide GLN G 504 and DLY G 505

Chain	Residue
C	GLU103
C	MET377
G	ASN501
G	HYP502
G	LYS503
G	TRP506
G	GLY507

site_id	AE9
Number of Residues	6
Details	binding site for Di-peptide DLY G 505 and TRP G 506

Chain	Residue
C	ASP104
G	U2M500
G	ASN501
G	LYS503
G	GLN504
G	GLY507

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	3
Details	ACT_SITE: ACT_SITE => ECO:0000250\|UniProtKB:Q13547

Chain	Residue	Details
A	HIS146
B	HIS146
C	HIS146

site_id	SWS_FT_FI2
Number of Residues	27
Details	BINDING: BINDING => ECO:0000269\|PubMed:37137925, ECO:0007744\|PDB:8BPA, ECO:0007744\|PDB:8BPB, ECO:0007744\|PDB:8BPC

Chain	Residue	Details
A	ASP179
B	ASP179
B	ASP181
B	HIS183
B	PHE192
B	THR195
B	VAL198
B	SER202
B	PHE203
B	ASP269
C	ASP179
A	ASP181
C	ASP181
C	HIS183
C	PHE192
C	THR195
C	VAL198
C	SER202
C	PHE203
C	ASP269
A	HIS183
A	PHE192
A	THR195
A	VAL198
A	SER202
A	PHE203
A	ASP269

site_id	SWS_FT_FI3
Number of Residues	3
Details	BINDING: BINDING => ECO:0000269\|PubMed:37137925, ECO:0007744\|PDB:8BPB, ECO:0007744\|PDB:8BPC

Chain	Residue	Details
A	TYR227
B	TYR227
C	TYR227

site_id	SWS_FT_FI4
Number of Residues	3
Details	MOD_RES: N6-acetyllysine; alternate => ECO:0000250\|UniProtKB:Q13547

Chain	Residue	Details
A	LYS79
B	LYS79
C	LYS79

site_id	SWS_FT_FI5
Number of Residues	3
Details	MOD_RES: N6-acetyllysine => ECO:0000250\|UniProtKB:Q13547

Chain	Residue	Details
A	LYS225
B	LYS225
C	LYS225

site_id	SWS_FT_FI6
Number of Residues	6
Details	MOD_RES: S-nitrosocysteine => ECO:0000250\|UniProtKB:P70288

Chain	Residue	Details
A	CYS266
A	CYS278
B	CYS266
B	CYS278
C	CYS266
C	CYS278

site_id	SWS_FT_FI7
Number of Residues	6
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0007744\|PubMed:28112733

Chain	Residue	Details
A	LYS79
B	LYS79
C	LYS79

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)