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Title :   CRYSTAL STRUCTURE OF D176N HDAC8 IN COMPLEX WITH M344

Authors :   C. Decroos, M. S. Lee, D. W. Christianson

Date :   23 Aug 15 (Deposition) - 03 Feb 16 (Release) - 17 Feb 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.94

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Histone Deacetylase 8, Arginase Fold, Deacetylase, Enzyme-Inhibitor Complex, Hydrolase-Hydrloase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. M. Gantt, C. Decroos, M. S. Lee, L. E. Gullett, C. M. Bowman, D. W. Christianson, C. A. Fierke
General Base-General Acid Catalysis In Human Histone Deacetylase 8.
Biochemistry V. 55 820 2016
PubMed-ID: 26806311 | Reference-DOI: 10.1021/ACS.BIOCHEM.5B01327

Molecule 1 - HISTONE DEACETYLASE 8
	Chains	:	A, B
	EC Number	:	3.5.1.98
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PHD2-XA-HIS
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	HDAC8, HDACL1, CDA07
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HD8

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	B3N	2	Ligand/Ion	4-(DIMETHYLAMINO)-N-[7-(HYDROXYAMINO)-7-OXOHEPTYL]BENZAMIDE
2	K	2	Ligand/Ion	POTASSIUM ION
3	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	B3N	1	Ligand/Ion	4-(DIMETHYLAMINO)-N-[7-(HYDROXYAMINO)-7-OXOHEPTYL]BENZAMIDE
2	K	-1	Ligand/Ion	POTASSIUM ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	B3N	1	Ligand/Ion	4-(DIMETHYLAMINO)-N-[7-(HYDROXYAMINO)-7-OXOHEPTYL]BENZAMIDE
2	K	-1	Ligand/Ion	POTASSIUM ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:189 , THR A:192 , VAL A:195 , TYR A:225 , HOH A:519 , HOH A:582	binding site for residue K A 401
2	AC2	SOFTWARE	TYR A:100 , HIS A:142 , HIS A:143 , GLY A:151 , PHE A:152 , ASP A:178 , HIS A:180 , ASP A:267 , GLY A:304 , TYR A:306 , ZN A:403 , HOH A:576 , LYS B:33 , PRO B:273 , TYR B:306 , B3N B:403	binding site for residue B3N A 402
3	AC3	SOFTWARE	ASP A:178 , HIS A:180 , ASP A:267 , B3N A:402	binding site for residue ZN A 403
4	AC4	SOFTWARE	ASP B:178 , HIS B:180 , ASP B:267 , B3N B:403	binding site for residue ZN B 401
5	AC5	SOFTWARE	PHE B:189 , THR B:192 , VAL B:195 , TYR B:225 , HOH B:508 , HOH B:582	binding site for residue K B 402
6	AC6	SOFTWARE	LYS A:33 , PHE A:152 , PRO A:273 , TYR A:306 , B3N A:402 , ASP B:101 , HIS B:142 , HIS B:143 , GLY B:151 , PHE B:152 , ASP B:178 , HIS B:180 , ASP B:267 , GLY B:304 , TYR B:306 , ZN B:401 , HOH B:587	binding site for residue B3N B 403

(no "SS Bond" information available for 5DC5)

Asymmetric Unit

No.	Residues
1	Phe A:208	-	Pro A:209
2	Gly A:341	-	Pro A:342
3	Phe B:208	-	Pro B:209
4	Gly B:341	-	Pro B:342

(no "SAP(SNP)/Variant" information available for 5DC5)

(no "PROSITE Motif" information available for 5DC5)

(no "Exon" information available for 5DC5)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:364
                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhhhhhh......hhhhhhhhhhhhhhhhhhheee.....hhhhhh...hhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhh.....eeeeee....hhhhhhhh.....eeeeeeee................hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeeee...............hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhh...........hhhhhh................hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dc5 A  14 LVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQDDDHPDSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVNLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVVIE 379
                                    23        33        43        53        63        73        83||      95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375    
                                                                                                 84|                                                                                                                                                                                                                                                                                                    
                                                                                                  87

Chain B from PDB  Type:PROTEIN  Length:355
                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhheee.....hhhhhh...hhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhh.....eeeeee....hhhhhhhh.....eeeeeeee................hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeeee...............hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhh............hhhhhh................hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dc5 B  14 LVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQESIEYGLDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVNLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVV 377
                                    23        33        43        53        63        73        83 ||    102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372     
                                                                                                  85|   98|                                                                                                                                                                                                                                                                                    
                                                                                                   93   101

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 5DC5)

(no "CATH Domain" information available for 5DC5)

(no "Pfam Domain" information available for 5DC5)

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	Cis Peptide Bonds
		Gly A:341 - Pro A:342	[ RasMol ]
		Gly B:341 - Pro B:342	[ RasMol ]
		Phe A:208 - Pro A:209	[ RasMol ]
		Phe B:208 - Pro B:209	[ RasMol ]

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		Biological Unit 2	[ Jena3D ]

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Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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Exons (0, 0)

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Gene Ontology (26, 26)

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