Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6WHN

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	HOH637
A	HOH643

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

Chain	Residue
A	LYS14
A	ASN100
A	ASP104
A	SER153
A	GLY154
A	PHE210
A	HOH509
A	HOH538
F	TRP506
F	GLY507

site_id	AC5
Number of Residues	3
Details	binding site for residue PG4 A 405

Chain	Residue
A	LYS71
A	ALA191
A	THR195

site_id	AC6
Number of Residues	6
Details	binding site for residue PG4 A 406

Chain	Residue
A	GLU340
A	TYR341
A	GLY343
A	HOH504
A	HOH511
A	HOH720

site_id	AC7
Number of Residues	6
Details	binding site for residue PG4 A 407

Chain	Residue
A	ASP23
A	ASN26
A	TYR27
A	GLY110
A	HOH581
A	HOH594

site_id	AC8
Number of Residues	6
Details	binding site for residue PGE A 408

Chain	Residue
A	ARG131
B	ASP23
B	ASN26
B	TYR27
B	ASP109
B	HOH776

site_id	AC9
Number of Residues	1
Details	binding site for residue PEG A 409

Chain	Residue
A	HIS38

site_id	AD1
Number of Residues	4
Details	binding site for residue ZN B 401

Chain	Residue
B	ASP181
B	HIS183
B	ASP269
G	U2M500

site_id	AD2
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	AD3
Number of Residues	6
Details	binding site for residue NA B 403

Chain	Residue
B	PHE192
B	THR195
B	VAL198
B	TYR227
B	HOH649
B	HOH651

site_id	AD4
Number of Residues	9
Details	binding site for residue NHE B 404

Chain	Residue
A	TYR59
A	LYS128
A	HOH590
B	ASP21
B	ASP23
B	TYR27
B	ARG60
B	LYS63
B	HOH610

site_id	AD5
Number of Residues	6
Details	binding site for residue PGE B 405

Chain	Residue
A	HOH512
B	ARG311
B	GLU340
B	TYR341
B	GLY343
B	HOH555

site_id	AD6
Number of Residues	3
Details	binding site for residue PG4 B 406

Chain	Residue
B	LYS284
C	GLU67
C	THR70

site_id	AD7
Number of Residues	6
Details	binding site for residue PGE B 407

Chain	Residue
B	LYS71
B	LEU166
B	ALA191
B	HOH734
B	HOH788
C	GLU91

site_id	AD8
Number of Residues	4
Details	binding site for residue ZN C 401

Chain	Residue
C	ASP181
C	HIS183
C	ASP269
H	U2M500

site_id	AD9
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	AE1
Number of Residues	6
Details	binding site for residue NA C 403

Chain	Residue
C	HOH586
C	HOH599
C	PHE192
C	THR195
C	VAL198
C	TYR227

site_id	AE2
Number of Residues	6
Details	binding site for residue PGE C 404

Chain	Residue
B	ASP345
C	ALA191
C	ARG197
C	HOH543
C	HOH597
C	HOH630

site_id	AE3
Number of Residues	6
Details	binding site for residue PG4 C 405

Chain	Residue
B	ASN354
C	LEU169
C	LYS170
C	TYR171
C	GLN173
C	ARG197

site_id	AE4
Number of Residues	6
Details	binding site for residue PGE C 406

Chain	Residue
C	ASP23
C	ASN26
C	TYR27
C	ASP109
C	HOH522
C	HOH638

site_id	AE5
Number of Residues	21
Details	binding site for Di-peptide U2M F 500 and GLY F 507

Chain	Residue
A	ASP104
A	HIS145
A	HIS146
A	GLY154
A	PHE155
A	ASP181
A	HIS183
A	PHE210
A	ASP269
A	LEU276
A	GLY306
A	TYR308
A	ZN401
A	NHE404
A	HOH509
F	ASN501
F	PRO502
F	DLY505
F	TRP506
F	HOH601
F	HOH602

site_id	AE6
Number of Residues	22
Details	binding site for Di-peptide U2M F 500 and ASN F 501

Chain	Residue
A	TYR7
A	HIS145
A	HIS146
A	GLY154
A	PHE155
A	ASP181
A	HIS183
A	PHE210
A	ASP269
A	LEU276
A	GLY306
A	TYR308
A	ZN401
A	HOH509
A	HOH682
F	PRO502
F	LYS503
F	GLN504
F	GLY507
F	HOH601
F	HOH602
F	HOH603

site_id	AE7
Number of Residues	11
Details	binding site for Di-peptide GLN F 504 and DLY F 505

Chain	Residue
A	ALA5
A	GLU103
A	ASP135
A	ASN297
F	ASN501
F	PRO502
F	LYS503
F	TRP506
F	GLY507
F	HOH601
F	HOH606

site_id	AE8
Number of Residues	13
Details	binding site for Di-peptide DLY F 505 and TRP F 506

Chain	Residue
A	LYS15
A	GLN132
A	GLN133
A	THR134
A	ASP135
A	ASN297
A	NHE404
A	HOH641
F	GLN504
F	GLY507
F	HOH604
F	HOH605
F	HOH606

site_id	AE9
Number of Residues	16
Details	binding site for Di-peptide U2M G 500 and GLY G 507

Chain	Residue
B	HIS145
B	HIS146
B	GLY154
B	PHE155
B	ASP181
B	HIS183
B	PHE210
B	ASP269
B	TYR308
B	ZN401
G	ASN501
G	PRO502
G	TRP506
G	HOH602
G	HOH603
G	HOH604

site_id	AF1
Number of Residues	20
Details	binding site for Di-peptide U2M G 500 and ASN G 501

Chain	Residue
B	HIS145
B	HIS146
B	GLY154
B	PHE155
B	ASP181
B	HIS183
B	PHE210
B	ASP269
B	LEU276
B	TYR308
B	ZN401
G	PRO502
G	LYS503
G	GLN504
G	DLY505
G	TRP506
G	GLY507
G	HOH601
G	HOH602
G	HOH604

site_id	AF2
Number of Residues	7
Details	binding site for Di-peptide GLN G 504 and DLY G 505

Chain	Residue
B	LYS13
B	GLY32
B	PRO34
G	ASN501
G	PRO502
G	LYS503
G	TRP506

site_id	AF3
Number of Residues	10
Details	binding site for Di-peptide DLY G 505 and TRP G 506

Chain	Residue
B	LYS13
B	HIS33
B	GLU103
B	ASP104
G	U2M500
G	ASN501
G	PRO502
G	LYS503
G	GLN504
G	GLY507

site_id	AF4
Number of Residues	18
Details	binding site for Di-peptide U2M H 500 and ASN H 501

Chain	Residue
C	ASP104
C	HIS145
C	HIS146
C	GLY154
C	PHE155
C	ASP181
C	HIS183
C	ASP269
C	LEU276
C	GLY306
C	TYR308
C	ZN401
H	PRO502
H	LYS503
H	GLN504
H	TRP506
H	GLY507
H	HOH601

site_id	AF5
Number of Residues	17
Details	binding site for Di-peptide U2M H 500 and GLY H 507

Chain	Residue
C	ASP104
C	HIS145
C	HIS146
C	GLY154
C	PHE155
C	ASP181
C	HIS183
C	PHE210
C	ASP269
C	GLY306
C	TYR308
C	ZN401
H	ASN501
H	PRO502
H	TRP506
H	HOH601
H	HOH602

site_id	AF6
Number of Residues	7
Details	binding site for Di-peptide GLN H 504 and DLY H 505

Chain	Residue
C	GLY32
C	ARG275
C	PRO379
H	ASN501
H	PRO502
H	LYS503
H	TRP506

site_id	AF7
Number of Residues	10
Details	binding site for Di-peptide DLY H 505 and TRP H 506

Chain	Residue
C	HIS33
C	GLU103
C	ASP104
C	PRO379
H	U2M500
H	ASN501
H	PRO502
H	LYS503
H	GLN504
H	GLY507

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	939
Details	Region: {"description":"Histone deacetylase"}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	3
Details	Active site: {"evidences":[{"source":"UniProtKB","id":"Q13547","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	9
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"O15379","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	27
Details	Binding site: {"evidences":[{"source":"PubMed","id":"37137925","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8BPA","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8BPB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8BPC","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PubMed","id":"37137925","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"8BPB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8BPC","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	3
Details	Modified residue: {"description":"N6-acetyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q13547","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	3
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"Q13547","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	6
Details	Modified residue: {"description":"S-nitrosocysteine","evidences":[{"source":"UniProtKB","id":"P70288","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	6
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

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