5D1B - JenaLib

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Title :   CRYSTAL STRUCTURE OF G117E HDAC8 IN COMPLEX WITH TSA

Authors :   C. Decroos, N. H. Christianson, L. E. Gullett, C. M. Bowman, K. E. Christ M. A. Deardorff, D. W. Christianson

Date :   04 Aug 15 (Deposition) - 21 Oct 15 (Release) - 11 Nov 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

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

Reference :   C. Decroos, N. H. Christianson, L. E. Gullett, C. M. Bowman, K. E. Christianson, M. A. Deardorff, D. W. Christianson
Biochemical And Structural Characterization Of Hdac8 Mutant Associated With Cornelia De Lange Syndrome Spectrum Disorders.
Biochemistry V. 54 6501 2015
PubMed-ID: 26463496 | Reference-DOI: 10.1021/ACS.BIOCHEM.5B00881

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, 8)

No.	Name	Count	Type	Full Name
1	K	4	Ligand/Ion	POTASSIUM ION
2	TSN	2	Ligand/Ion	TRICHOSTATIN A
3	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	K	-1	Ligand/Ion	POTASSIUM ION
2	TSN	1	Ligand/Ion	TRICHOSTATIN A
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	K	-1	Ligand/Ion	POTASSIUM ION
2	TSN	1	Ligand/Ion	TRICHOSTATIN A
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:178 , HIS A:180 , ASP A:267 , TSN A:404	binding site for residue ZN A 401
2	AC2	SOFTWARE	ASP A:176 , ASP A:178 , HIS A:180 , SER A:199 , LEU A:200 , HIS A:201	binding site for residue K A 402
3	AC3	SOFTWARE	PHE A:189 , THR A:192 , VAL A:195 , TYR A:225	binding site for residue K A 403
4	AC4	SOFTWARE	HIS A:142 , HIS A:143 , PHE A:152 , ASP A:178 , HIS A:180 , ASP A:267 , MET A:274 , TYR A:306 , ZN A:401 , PRO B:273 , MET B:274 , TYR B:306	binding site for residue TSN A 404
5	AC5	SOFTWARE	ASP B:178 , HIS B:180 , ASP B:267 , TSN B:404	binding site for residue ZN B 401
6	AC6	SOFTWARE	ASP B:176 , ASP B:178 , HIS B:180 , SER B:199 , LEU B:200 , HIS B:201	binding site for residue K B 402
7	AC7	SOFTWARE	PHE B:189 , THR B:192 , VAL B:195 , TYR B:225 , SER B:226 , HOH B:501 , HOH B:502	binding site for residue K B 403
8	AC8	SOFTWARE	MET A:274 , TYR A:306 , TYR B:100 , HIS B:142 , HIS B:143 , PHE B:152 , ASP B:178 , HIS B:180 , PHE B:208 , ASP B:267 , MET B:274 , TYR B:306 , ZN B:401	binding site for residue TSN B 404

(no "SS Bond" information available for 5D1B)

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 5D1B)

(no "PROSITE Motif" information available for 5D1B)

(no "Exon" information available for 5D1B)

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:356
                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhheee.....hhhhhh...hhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhh.....eeeee.....hhhhhhhh.....eeeeeeee................hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee................hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhh...........hhhhhh................hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d1b A  14 LVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGEYGLGYDCPATEGIFDYAAAIGEATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVV 377
                                    23        33        43        53        63        73        83  ||   101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371      
                                                                                                   86|                                                                                                                                                                                                                                                                                          
                                                                                                    95

Chain B from PDB  Type:PROTEIN  Length:365
                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhhhhhh......hhhhhhhhhhhhhhhhhhheee.....hhhhhh...hhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhh.....eeeee.....hhhhhhhh.....eeeeeeee................hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee................hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhh...........hhhhhh................hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d1b B  14 LVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGIFDYAAAIGEATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVVI 378
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373

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 5D1B)

(no "CATH Domain" information available for 5D1B)

(no "Pfam Domain" information available for 5D1B)

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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, 8)

Sites (8, 8)

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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