Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5WGM

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with ACY-1083

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000118	cellular_component	histone deacetylase complex
A	0004407	molecular_function	histone deacetylase activity
A	0006325	biological_process	chromatin organization
A	0016575	biological_process	histone deacetylation
B	0000118	cellular_component	histone deacetylase complex
B	0004407	molecular_function	histone deacetylase activity
B	0006325	biological_process	chromatin organization
B	0016575	biological_process	histone deacetylation
C	0000118	cellular_component	histone deacetylase complex
C	0004407	molecular_function	histone deacetylase activity
C	0006325	biological_process	chromatin organization
C	0016575	biological_process	histone deacetylation

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	binding site for residue ZN A 801

Chain	Residue
A	ASP612
A	HIS614
A	ASP705
A	AH7804
A	HOH923

site_id	AC2
Number of Residues	5
Details	binding site for residue K A 802

Chain	Residue
A	LEU634
A	ASP610
A	ASP612
A	HIS614
A	SER633

site_id	AC3
Number of Residues	5
Details	binding site for residue K A 803

Chain	Residue
A	PHE623
A	ASP626
A	VAL629
A	TYR662
A	HOH934

site_id	AC4
Number of Residues	23
Details	binding site for residue AH7 A 804

Chain	Residue
A	HIS463
A	PRO464
A	SER531
A	HIS574
A	GLY582
A	PHE583
A	ASP612
A	HIS614
A	PHE643
A	ASP705
A	LEU712
A	GLY743
A	TYR745
A	ZN801
A	EDO807
A	HOH923
A	HOH1154
C	GLY438
C	GLY439
C	SER440
C	SER441
C	PRO442
C	ARG562

site_id	AC5
Number of Residues	4
Details	binding site for residue EDO A 805

Chain	Residue
A	PHE474
A	ARG488
A	HOH1117
A	HOH1147

site_id	AC6
Number of Residues	9
Details	binding site for residue EDO A 806

Chain	Residue
A	ASN523
A	GLY526
A	ASP527
A	ILE532
A	HOH980
A	HOH1044
C	ASN436
C	ALA437
C	GLY438

site_id	AC7
Number of Residues	4
Details	binding site for residue EDO A 807

Chain	Residue
A	ASN530
A	PRO644
A	ASN645
A	AH7804

site_id	AC8
Number of Residues	4
Details	binding site for residue EDO A 808

Chain	Residue
A	LEU525
A	GLU528
A	TYR529
A	HOH1007

site_id	AC9
Number of Residues	8
Details	binding site for residue EDO A 809

Chain	Residue
A	TYR448
A	ASP449
A	ARG488
A	ALA491
A	HOH912
A	HOH915
A	HOH965
A	HOH1138

site_id	AD1
Number of Residues	6
Details	binding site for residue EDO A 810

Chain	Residue
A	GLN468
A	HOH903
A	HOH963
B	GLN468
B	EDO806
B	HOH919

site_id	AD2
Number of Residues	8
Details	binding site for residue EDO A 812

Chain	Residue
A	ARG636
A	ALA641
A	PHE642
A	HOH918
A	HOH932
A	HOH1163
C	MET730
C	GLY763

site_id	AD3
Number of Residues	6
Details	binding site for residue EDO A 813

Chain	Residue
A	ARG708
A	GLY709
A	ASP710
A	GLY714
A	PHE715
A	HOH921

site_id	AD4
Number of Residues	4
Details	binding site for residue EDO A 814

Chain	Residue
A	ALA500
A	LEU501
A	LYS577
A	HOH916

site_id	AD5
Number of Residues	2
Details	binding site for residue EDO A 815

Chain	Residue
A	ASP521
A	ARG524

site_id	AD6
Number of Residues	7
Details	binding site for residue PGE A 816

Chain	Residue
B	SER749
A	ARG476
A	GLU479
A	HOH908
B	ARG708
B	GLY709
B	ASN746

site_id	AD7
Number of Residues	9
Details	binding site for residue PEG A 817

Chain	Residue
A	SER475
A	GLU478
A	HOH905
A	HOH910
A	HOH914
A	HOH968
A	HOH1124
B	LEU466
B	LEU747

site_id	AD8
Number of Residues	5
Details	binding site for residue ZN B 801

Chain	Residue
B	ASP612
B	HIS614
B	ASP705
B	AH7804
B	HOH901

site_id	AD9
Number of Residues	5
Details	binding site for residue K B 802

Chain	Residue
B	ASP610
B	ASP612
B	HIS614
B	SER633
B	LEU634

site_id	AE1
Number of Residues	5
Details	binding site for residue K B 803

Chain	Residue
B	PHE623
B	ASP626
B	VAL629
B	TYR662
B	HOH984

site_id	AE2
Number of Residues	20
Details	binding site for residue AH7 B 804

Chain	Residue
A	GLY438
A	GLY439
A	SER440
A	SER441
A	PRO442
B	HIS463
B	PRO464
B	SER531
B	HIS574
B	GLY582
B	PHE583
B	ASP612
B	HIS614
B	PHE643
B	ASP705
B	GLY743
B	TYR745
B	ZN801
B	HOH901
B	HOH968

site_id	AE3
Number of Residues	6
Details	binding site for residue EDO B 805

Chain	Residue
B	GLU498
B	GLN554
B	TYR595
B	TYR595
B	HOH966
B	HOH1051

site_id	AE4
Number of Residues	7
Details	binding site for residue EDO B 806

Chain	Residue
A	EDO810
A	HOH1132
B	SER471
B	ARG472
B	SER475
B	HOH918
B	HOH919

site_id	AE5
Number of Residues	4
Details	binding site for residue EDO B 807

Chain	Residue
B	TYR448
B	PHE474
B	ARG488
B	HOH1061

site_id	AE6
Number of Residues	5
Details	binding site for residue EDO B 808

Chain	Residue
B	TYR637
B	ASP639
B	GLU647
B	ASN650
B	HOH906

site_id	AE7
Number of Residues	5
Details	binding site for residue EDO B 809

Chain	Residue
B	HIS456
B	MET458
B	SER535
B	ASN536
B	GLU537

site_id	AE8
Number of Residues	4
Details	binding site for residue EDO B 810

Chain	Residue
B	SER509
B	LYS512
B	SER513
B	HOH902

site_id	AE9
Number of Residues	6
Details	binding site for residue EDO B 811

Chain	Residue
B	PRO442
B	ARG485
B	LEU762
B	HOH916
B	HOH1013
B	HOH1059

site_id	AF1
Number of Residues	4
Details	binding site for residue EDO B 812

Chain	Residue
B	MET756
B	HOH928
B	HOH986
B	HOH1019

site_id	AF2
Number of Residues	5
Details	binding site for residue EDO B 813

Chain	Residue
B	ILE510
B	GLU528
B	TYR529
B	HOH904
B	HOH1057

site_id	AF3
Number of Residues	1
Details	binding site for residue EDO B 814

Chain	Residue
B	ARG451

site_id	AF4
Number of Residues	2
Details	binding site for residue EDO B 815

Chain	Residue
B	HIS684
B	ASN784

site_id	AF5
Number of Residues	8
Details	binding site for residue EDO B 816

Chain	Residue
B	GLY763
B	ASP764
B	SER765
B	HOH976
B	HOH1120
C	ARG636
C	LYS672
C	GLY714

site_id	AF6
Number of Residues	1
Details	binding site for residue EDO B 817

Chain	Residue
B	HOH996

site_id	AF7
Number of Residues	6
Details	binding site for residue EDO B 818

Chain	Residue
B	PHE682
B	HIS683
B	MET687
B	GLN728
B	HOH953
B	HOH1040

site_id	AF8
Number of Residues	2
Details	binding site for residue EDO B 819

Chain	Residue
B	ASN784
B	ARG788

site_id	AF9
Number of Residues	5
Details	binding site for residue ZN C 801

Chain	Residue
C	ASP612
C	HIS614
C	ASP705
C	AH7804
C	HOH907

site_id	AG1
Number of Residues	5
Details	binding site for residue K C 802

Chain	Residue
C	ASP610
C	ASP612
C	HIS614
C	SER633
C	LEU634

site_id	AG2
Number of Residues	5
Details	binding site for residue K C 803

Chain	Residue
C	PHE623
C	ASP626
C	VAL629
C	TYR662
C	HOH992

site_id	AG3
Number of Residues	21
Details	binding site for residue AH7 C 804

Chain	Residue
B	GLY438
B	GLY439
B	SER440
B	SER441
B	ARG562
C	HIS463
C	PRO464
C	SER531
C	HIS574
C	GLY582
C	PHE583
C	ASP612
C	HIS614
C	PHE643
C	ASP705
C	GLY743
C	TYR745
C	ZN801
C	EDO813
C	HOH907
C	HOH1119

site_id	AG4
Number of Residues	10
Details	binding site for residue EDO C 805

Chain	Residue
C	SER440
C	SER441
C	PRO442
C	ILE443
C	GLY559
C	GLN560
C	VAL561
C	ARG562
C	HOH1087
C	HOH1121

site_id	AG5
Number of Residues	7
Details	binding site for residue EDO C 806

Chain	Residue
C	GLN468
C	SER471
C	ARG472
C	SER475
C	HOH997
C	HOH1081
C	HOH1116

site_id	AG6
Number of Residues	5
Details	binding site for residue EDO C 807

Chain	Residue
C	HIS456
C	MET458
C	SER535
C	ASN536
C	GLU537

site_id	AG7
Number of Residues	4
Details	binding site for residue EDO C 808

Chain	Residue
C	PHE474
C	ARG488
C	HOH945
C	HOH1178

site_id	AG8
Number of Residues	5
Details	binding site for residue EDO C 809

Chain	Residue
C	ARG476
C	ARG708
C	ASN746
C	SER749
C	EDO815

site_id	AG9
Number of Residues	4
Details	binding site for residue EDO C 810

Chain	Residue
C	MET453
C	PRO467
C	HOH1129
C	HOH1150

site_id	AH1
Number of Residues	4
Details	binding site for residue EDO C 811

Chain	Residue
C	ALA500
C	LEU501
C	HIS503
C	HOH996

site_id	AH2
Number of Residues	5
Details	binding site for residue EDO C 813

Chain	Residue
C	ASN530
C	PHE643
C	PRO644
C	ASN645
C	AH7804

site_id	AH3
Number of Residues	2
Details	binding site for residue EDO C 814

Chain	Residue
C	HIS724
C	LEU769

site_id	AH4
Number of Residues	4
Details	binding site for residue EDO C 815

Chain	Residue
C	PRO719
C	SER749
C	GLU752
C	EDO809

site_id	AH5
Number of Residues	9
Details	binding site for residue PGE C 816

Chain	Residue
C	PRO442
C	ILE443
C	THR444
C	ARG485
C	LEU761
C	LEU762
C	HOH986
C	HOH1015
C	HOH1166

site_id	AH6
Number of Residues	6
Details	binding site for residue PEG C 817

Chain	Residue
C	ARG605
C	ASP627
C	TYR662
C	PHE693
C	HOH905
C	HOH1036

site_id	AH7
Number of Residues	33
Details	binding site for Di-peptide EDO A 811 and GLU C 497

Chain	Residue
A	ARG492
A	ARG492
A	LEU493
A	THR495
A	GLU496
A	GLU498
A	LEU499
A	ALA500
A	LEU501
A	HOH948
A	HOH949
A	HOH960
A	HOH986
A	HOH1086
A	HOH1123
A	HOH1144
C	ARG492
C	THR495
C	GLU496
C	GLU498
C	LEU499
C	ALA500
C	LEU501
C	HIS503
C	HOH934
C	HOH934
C	HOH936
C	HOH942
C	HOH996
C	HOH1006
C	HOH1068
C	HOH1078
C	HOH1078

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