Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6XDM

STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH AN ARYL KETONE INHIBITOR

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	ASP177
A	HIS179
A	ASP265
A	V1D411

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

Chain	Residue
A	ASP175
A	ASP177
A	HIS179
A	SER198
A	PHE199

site_id	AC3
Number of Residues	6
Details	binding site for residue CA A 403

Chain	Residue
A	PHE188
A	THR191
A	VAL194
A	TYR223
A	HOH550
A	HOH717

site_id	AC4
Number of Residues	6
Details	binding site for residue SO4 A 404

Chain	Residue
A	GLU87
A	TYR88
A	LYS90
A	GLN91
A	HOH504
A	HOH684

site_id	AC5
Number of Residues	9
Details	binding site for residue SO4 A 405

Chain	Residue
A	ARG213
A	ARG366
A	HOH505
A	HOH526
A	HOH568
A	HOH722
B	PRO330
B	TYR331
B	HOH664

site_id	AC6
Number of Residues	5
Details	binding site for residue SO4 A 406

Chain	Residue
A	SER70
A	ASP71
A	LYS145
A	HOH502
A	HOH748

site_id	AC7
Number of Residues	3
Details	binding site for residue SO4 A 407

Chain	Residue
A	THR305
A	ARG307
A	HOH599

site_id	AC8
Number of Residues	4
Details	binding site for residue PEG A 408

Chain	Residue
A	ASP19
A	ASN22
A	TYR23
A	ASP105

site_id	AC9
Number of Residues	3
Details	binding site for residue PEG A 409

Chain	Residue
A	ARG307
A	GLU336
A	GLY339

site_id	AD1
Number of Residues	2
Details	binding site for residue PEG A 410

Chain	Residue
A	TYR24
A	HIS34

site_id	AD2
Number of Residues	20
Details	binding site for residue V1D A 411

Chain	Residue
A	GLY28
A	PRO30
A	MET31
A	ASP100
A	GLY139
A	LEU140
A	HIS141
A	HIS142
A	GLY150
A	PHE151
A	CYS152
A	ASP177
A	HIS179
A	ASP265
A	GLY302
A	TYR304
A	ZN401
A	HOH615
A	HOH667
A	HOH773

site_id	AD3
Number of Residues	4
Details	binding site for residue ZN B 401

Chain	Residue
B	ASP177
B	HIS179
B	ASP265
B	V1D408

site_id	AD4
Number of Residues	5
Details	binding site for residue CA B 402

Chain	Residue
B	ASP175
B	ASP177
B	HIS179
B	SER198
B	PHE199

site_id	AD5
Number of Residues	6
Details	binding site for residue CA B 403

Chain	Residue
B	PHE188
B	THR191
B	VAL194
B	TYR223
B	HOH672
B	HOH745

site_id	AD6
Number of Residues	6
Details	binding site for residue SO4 B 404

Chain	Residue
B	GLU87
B	TYR88
B	LYS90
B	GLN91
B	HOH510
B	HOH722

site_id	AD7
Number of Residues	4
Details	binding site for residue SO4 B 405

Chain	Residue
B	ARG307
B	HOH502
B	HOH628
B	HOH717

site_id	AD8
Number of Residues	3
Details	binding site for residue PEG B 406

Chain	Residue
B	ASN350
B	HOH816
C	PEG408

site_id	AD9
Number of Residues	4
Details	binding site for residue PEG B 407

Chain	Residue
B	ASN22
B	TYR23
B	HOH506
B	HOH588

site_id	AE1
Number of Residues	21
Details	binding site for residue V1D B 408

Chain	Residue
B	GLY28
B	PRO30
B	MET31
B	ASP100
B	GLY139
B	HIS141
B	HIS142
B	GLY150
B	PHE151
B	CYS152
B	ASP177
B	HIS179
B	PHE206
B	ASP265
B	GLY301
B	GLY302
B	TYR304
B	ZN401
B	HOH537
B	HOH579
B	HOH814

site_id	AE2
Number of Residues	4
Details	binding site for residue ZN C 401

Chain	Residue
C	ASP177
C	HIS179
C	ASP265
C	V1D410

site_id	AE3
Number of Residues	6
Details	binding site for residue CA C 402

Chain	Residue
C	PHE188
C	THR191
C	VAL194
C	TYR223
C	HOH617
C	HOH664

site_id	AE4
Number of Residues	5
Details	binding site for residue CA C 403

Chain	Residue
C	ASP175
C	ASP177
C	HIS179
C	SER198
C	PHE199

site_id	AE5
Number of Residues	3
Details	binding site for residue SO4 C 404

Chain	Residue
A	ARG81
C	ARG230
C	LYS362

site_id	AE6
Number of Residues	7
Details	binding site for residue SO4 C 405

Chain	Residue
C	ARG271
C	TYR304
C	THR305
C	ILE306
C	ARG307
C	TYR337
C	HOH508

site_id	AE7
Number of Residues	5
Details	binding site for residue SO4 C 406

Chain	Residue
B	SER347
B	PRO348
C	LYS67
C	LYS166
C	HOH510

site_id	AE8
Number of Residues	4
Details	binding site for residue SO4 C 407

Chain	Residue
C	HIS58
C	LYS59
C	HOH509
C	HOH578

site_id	AE9
Number of Residues	7
Details	binding site for residue PEG C 408

Chain	Residue
B	ASN350
B	PEG406
C	LEU165
C	LYS166
C	TYR167
C	GLN169
C	ARG193

site_id	AF1
Number of Residues	6
Details	binding site for residue PEG C 409

Chain	Residue
C	PHE206
C	PRO207
C	GLY208
C	HOH575
C	HOH587
C	HOH766

site_id	AF2
Number of Residues	20
Details	binding site for residue V1D C 410

Chain	Residue
C	GLY28
C	PRO30
C	MET31
C	ASP100
C	GLY139
C	LEU140
C	HIS141
C	HIS142
C	GLY150
C	PHE151
C	CYS152
C	ASP177
C	HIS179
C	PHE206
C	ASP265
C	GLY301
C	GLY302
C	TYR304
C	ZN401
C	HOH521

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
B	HIS142
C	HIS142
A	HIS142

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	PHE188
A	THR191
A	VAL194
A	SER198
A	PHE199
A	ASP265
B	ASP175
B	ASP177
B	HIS179
B	PHE188
B	THR191
B	VAL194
B	SER198
B	PHE199
B	ASP265
C	ASP175
C	ASP177
C	HIS179
C	PHE188
C	THR191
C	VAL194
C	SER198
C	PHE199
C	ASP265
A	ASP177
A	HIS179
A	ASP175

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
B	TYR223
C	TYR223
A	TYR223

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

Chain	Residue	Details
C	LYS75
A	LYS75
B	LYS75

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

Chain	Residue	Details
B	LYS221
C	LYS221
A	LYS221

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

Chain	Residue	Details
A	CYS262
A	CYS274
B	CYS262
B	CYS274
C	CYS262
C	CYS274

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	LYS75
B	LYS75
C	LYS75

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