Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6WHO

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
F	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	6
Details	binding site for residue NA A 403

Chain	Residue
A	PHE192
A	THR195
A	VAL198
A	TYR227
A	HOH531
A	HOH605

site_id	AC4
Number of Residues	10
Details	binding site for residue NHE A 404

Chain	Residue
A	TYR59
A	LYS128
A	HOH548
B	ASP21
B	GLY22
B	ASP23
B	TYR27
B	ARG60
B	GLU113
B	LEU117

site_id	AC5
Number of Residues	10
Details	binding site for residue NHE A 405

Chain	Residue
A	LYS13
A	LYS14
A	LYS15
A	ASN100
A	ASP104
A	SER153
A	GLY154
A	PHE210
A	HOH541
F	GLY507

site_id	AC6
Number of Residues	1
Details	binding site for residue PG4 A 406

Chain	Residue
A	ALA191

site_id	AC7
Number of Residues	3
Details	binding site for residue PGE A 407

Chain	Residue
A	ARG311
A	GLU340
A	GLY343

site_id	AC8
Number of Residues	3
Details	binding site for residue PG4 A 408

Chain	Residue
A	ASN26
A	TYR27
A	ASP109

site_id	AC9
Number of Residues	4
Details	binding site for residue ZN B 401

Chain	Residue
B	ASP181
B	HIS183
B	ASP269
G	U2M500

site_id	AD1
Number of Residues	5
Details	binding site for residue NA B 402

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

site_id	AD2
Number of Residues	6
Details	binding site for residue NA B 403

Chain	Residue
B	PHE192
B	THR195
B	VAL198
B	TYR227
B	HOH516
B	HOH557

site_id	AD3
Number of Residues	4
Details	binding site for residue PG4 B 404

Chain	Residue
A	ARG131
B	ASN26
B	TYR27
B	ASP109

site_id	AD4
Number of Residues	5
Details	binding site for residue PGE B 405

Chain	Residue
B	ARG311
B	GLU340
B	TYR341
B	GLY343
B	HOH593

site_id	AD5
Number of Residues	4
Details	binding site for residue PG4 B 406

Chain	Residue
B	LYS284
B	HIS349
C	GLU67
C	LYS71

site_id	AD6
Number of Residues	5
Details	binding site for residue PG4 B 407

Chain	Residue
B	ASN354
C	LYS170
C	TYR171
C	GLN173
C	ARG197

site_id	AD7
Number of Residues	4
Details	binding site for residue ZN C 401

Chain	Residue
C	ASP181
C	HIS183
C	ASP269
H	U2M500

site_id	AD8
Number of Residues	5
Details	binding site for residue NA C 402

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

site_id	AD9
Number of Residues	6
Details	binding site for residue NA C 403

Chain	Residue
C	PHE192
C	THR195
C	VAL198
C	TYR227
C	HOH536
C	HOH538

site_id	AE1
Number of Residues	3
Details	binding site for residue PGE C 404

Chain	Residue
C	ALA191
C	ARG197
C	HOH508

site_id	AE2
Number of Residues	4
Details	binding site for residue PG4 C 405

Chain	Residue
B	LYS71
B	TYR72
B	ALA191
C	GLU91

site_id	AE3
Number of Residues	3
Details	binding site for residue PGE C 406

Chain	Residue
C	ASP109
C	ASP23
C	ASN26

site_id	AE4
Number of Residues	17
Details	binding site for Di-peptide U2M F 500 and GLY F 507

Chain	Residue
A	ASP104
A	HIS146
A	GLY154
A	PHE155
A	HIS183
A	PHE210
A	ASP269
A	LEU276
A	TYR308
A	ZN401
A	NHE405
F	ASN501
F	PRO502
F	DLY505
F	TRP506
F	HOH601
F	HOH602

site_id	AE5
Number of Residues	17
Details	binding site for Di-peptide U2M F 500 and ASN F 501

Chain	Residue
A	TYR7
A	HIS146
A	GLY154
A	PHE155
A	HIS183
A	PHE210
A	ASP269
A	LEU276
A	TYR308
A	ZN401
F	PRO502
F	GLU503
F	GLN504
F	GLY507
F	HOH601
F	HOH602
F	HOH603

site_id	AE6
Number of Residues	9
Details	binding site for Di-peptide GLN F 504 and DLY F 505

Chain	Residue
A	TYR7
A	GLU103
A	ASP135
F	ASN501
F	PRO502
F	GLU503
F	TRP506
F	GLY507
F	HOH601

site_id	AE7
Number of Residues	9
Details	binding site for Di-peptide DLY F 505 and TRP F 506

Chain	Residue
A	LYS15
A	GLU103
A	GLN132
A	GLN133
A	THR134
A	ASP135
A	HOH514
F	GLN504
F	GLY507

site_id	AE8
Number of Residues	15
Details	binding site for Di-peptide U2M G 500 and GLY G 507

Chain	Residue
B	ASP104
B	HIS146
B	GLY154
B	PHE155
B	ASP181
B	HIS183
B	PHE210
B	ASP269
B	GLY306
B	TYR308
B	ZN401
B	HOH568
G	ASN501
G	PRO502
G	TRP506

site_id	AE9
Number of Residues	21
Details	binding site for Di-peptide U2M G 500 and ASN G 501

Chain	Residue
B	PRO34
B	ASP104
B	HIS146
B	GLY154
B	PHE155
B	ASP181
B	HIS183
B	PHE210
B	ASP269
B	LEU276
B	GLY306
B	TYR308
B	ZN401
B	HOH538
B	HOH568
G	PRO502
G	GLU503
G	GLN504
G	DLY505
G	TRP506
G	GLY507

site_id	AF1
Number of Residues	6
Details	binding site for Di-peptide GLN G 504 and DLY G 505

Chain	Residue
B	LYS14
B	HOH538
G	ASN501
G	PRO502
G	GLU503
G	TRP506

site_id	AF2
Number of Residues	5
Details	binding site for Di-peptide DLY G 505 and TRP G 506

Chain	Residue
B	LYS14
G	U2M500
G	ASN501
G	GLN504
G	GLY507

site_id	AF3
Number of Residues	14
Details	binding site for Di-peptide U2M H 500 and ASN H 501

Chain	Residue
C	ASP104
C	HIS146
C	GLY154
C	PHE155
C	HIS183
C	PHE210
C	LEU276
C	TYR308
C	ZN401
C	HOH510
H	PRO502
H	GLU503
H	GLN504
H	GLY506

site_id	AF4
Number of Residues	13
Details	binding site for Di-peptide U2M H 500 and GLY H 506

Chain	Residue
C	ASP104
C	HIS146
C	GLY154
C	PHE155
C	HIS183
C	PHE210
C	TYR308
C	ZN401
C	HOH510
H	ASN501
H	PRO502
H	TRP505
H	HOH602

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)