5THS - JenaLib

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Title :   CRYSTAL STRUCTURE OF G302A HDAC8 IN COMPLEX WITH M344

Authors :   N. J. Porter, D. W. Christianson

Date :   30 Sep 16 (Deposition) - 21 Dec 16 (Release) - 21 Dec 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Zinc Histone Deacetylase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. J. Porter, N. H. Christianson, C. Decroos, D. W. Christianson
Structural And Functional Influence Of The Glycine-Rich Loo G302Gggy On The Catalytic Tyrosine Of Histone Deacetylase 8
Biochemistry V. 55 6718 2016
PubMed: search | Reference-DOI: 10.1021/ACS.BIOCHEM.6B01014

Molecule 1 - HISTONE DEACETYLASE 8
	Chains	:	A, B
	EC Number	:	3.5.1.98
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET20B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	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 (4, 21)

No.	Name	Count	Type	Full Name
1	B3N	2	Ligand/Ion	4-(DIMETHYLAMINO)-N-[7-(HYDROXYAMINO)-7-OXOHEPTYL]BENZAMIDE
2	EDO	13	Ligand/Ion	1,2-ETHANEDIOL
3	K	4	Ligand/Ion	POTASSIUM ION
4	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 8)

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

Biological Unit 2 (2, 7)

No.	Name	Count	Type	Full Name
1	B3N	1	Ligand/Ion	4-(DIMETHYLAMINO)-N-[7-(HYDROXYAMINO)-7-OXOHEPTYL]BENZAMIDE
2	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
3	K	-1	Ligand/Ion	POTASSIUM ION
4	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (21, 21)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:178 , HIS A:180 , ASP A:267 , B3N A:404	binding site for residue ZN A 401
02	AC2	SOFTWARE	ASP A:176 , ASP A:178 , HIS A:180 , SER A:199 , LEU A:200	binding site for residue K A 402
03	AC3	SOFTWARE	PHE A:189 , THR A:192 , VAL A:195 , TYR A:225 , HOH A:515 , HOH A:600	binding site for residue K A 403
04	AC4	SOFTWARE	ASP A:101 , HIS A:142 , HIS A:143 , ASP A:178 , HIS A:180 , ASP A:267 , TYR A:306 , ZN A:401 , EDO A:411 , HOH A:595 , HOH A:597 , PHE B:152 , PRO B:273 , TYR B:306 , B3N B:404	binding site for residue B3N A 404
05	AC5	SOFTWARE	ALA A:270 , ASN A:310 , ILE A:348 , THR A:349 , HOH A:551	binding site for residue EDO A 405
06	AC6	SOFTWARE	PRO A:281 , VAL A:282 , TYR A:317 , LEU A:346 , GLU A:347 , ILE A:348 , HOH A:564	binding site for residue EDO A 406
07	AC7	SOFTWARE	VAL A:133 , LEU A:292 , GLN A:295 , LEU A:296 , THR A:298	binding site for residue EDO A 407
08	AC8	SOFTWARE	ASP A:237 , VAL A:282 , LYS A:286 , HOH A:501 , HOH A:526	binding site for residue EDO A 408
09	AC9	SOFTWARE	LYS A:239 , ASP A:355 , HOH A:541	binding site for residue EDO A 409
10	AD1	SOFTWARE	TYR A:111 , ILE A:115 , TRP A:141 , CYS A:153 , TYR A:154 , LEU A:155	binding site for residue EDO A 410
11	AD2	SOFTWARE	GLY A:140 , TRP A:141 , GLY A:303 , TYR A:306 , B3N A:404 , HOH A:575	binding site for residue EDO A 411
12	AD3	SOFTWARE	ASP B:178 , HIS B:180 , ASP B:267 , B3N B:404	binding site for residue ZN B 401
13	AD4	SOFTWARE	ASP B:176 , ASP B:178 , HIS B:180 , SER B:199 , LEU B:200	binding site for residue K B 402
14	AD5	SOFTWARE	PHE B:189 , THR B:192 , VAL B:195 , TYR B:225 , HOH B:520 , HOH B:590	binding site for residue K B 403
15	AD6	SOFTWARE	PHE A:152 , PRO A:273 , MET A:274 , TYR A:306 , B3N A:404 , HIS B:142 , HIS B:143 , PHE B:152 , ASP B:178 , HIS B:180 , ASP B:267 , GLY B:304 , TYR B:306 , ZN B:401 , EDO B:405 , EDO B:408 , HOH B:562	binding site for residue B3N B 404
16	AD7	SOFTWARE	GLY B:140 , TRP B:141 , HIS B:142 , GLY B:303 , GLY B:304 , TYR B:306 , B3N B:404	binding site for residue EDO B 405
17	AD8	SOFTWARE	PRO B:281 , TYR B:317 , LEU B:346 , GLU B:347 , ILE B:348 , HOH B:506	binding site for residue EDO B 406
18	AD9	SOFTWARE	ILE B:34 , ARG B:37 , ALA B:38 , VAL B:41 , TRP B:137 , SER B:138 , TRP B:315	binding site for residue EDO B 407
19	AE1	SOFTWARE	SER B:150 , GLY B:151 , PHE B:208 , B3N B:404	binding site for residue EDO B 408
20	AE2	SOFTWARE	LYS B:289 , GLY B:324 , LYS B:325	binding site for residue EDO B 409
21	AE3	SOFTWARE	TRP B:141 , PHE B:152 , TYR B:154 , LEU B:155	binding site for residue EDO B 410

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

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 5THS)

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

(no "Exon" information available for 5THS)

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
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Chain A from PDB  Type:PROTEIN  Length:364
                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhheee.....hhhhhh...hhhhhhhhhhhh........hhhhhh.........hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhh.....eeeee.....hhhhhhhh.....eeeeeeee................hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh..........hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhh...........hhhhhh................hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ths A  14 LVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILAGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVV 377
                                    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

Chain B from PDB  Type:PROTEIN  Length:357
                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhhhhhh......hhhhhhhhhhhhh.hhhhheee.....hhhhhh...hhhhhhhhhhhhhhh.hhhhh.......hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhh.....eeeee.....hhhhhhhh.....eeeeeeee................hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee................hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhh...........hhhhhh................hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ths B  14 LVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDHPDSIEYGLATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILAGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVV 377
                                    23        33        43        53        63        73        83   ||   95  ||   110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       
                                                                                                    87|      98|                                                                                                                                                                                                                                                                                 
                                                                                                     90      104

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 5THS)

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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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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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 21)

Sites (21, 21)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

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Exons (0, 0)

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Gene Ontology (26, 26)

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