4RN2 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF S39D HDAC8 IN COMPLEX WITH A LARGAZOLE ANALOGUE.

Authors :   C. Decroos, D. W. Christianson

Date :   22 Oct 14 (Deposition) - 08 Apr 15 (Release) - 22 Apr 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.39

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)

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

Reference :   C. Decroos, D. J. Clausen, B. E. Haines, O. Wiest, R. M. Williams, D. W. Christianson
Variable Active Site Loop Conformations Accommodate The Binding Of Macrocyclic Largazole Analogues To Hdac8.
Biochemistry V. 54 2126 2015
PubMed-ID: 25793284 | Reference-DOI: 10.1021/ACS.BIOCHEM.5B00010

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
	Fragment	:	S39D HDAC8
	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
Biological Unit 3 (1x)	:	A	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	L7G	2	Ligand/Ion	(5R,8S,11S)-5-METHYL-8-(PROPAN-2-YL)-11-[(1E)-4-SULFANYLBUT-1-EN-1-YL]-3-THIA-7,10,14,17,21-PENTAAZATRICYCLO[14.3.1.1~2,5~]HENICOSA-1(20),2(21),16,18-TETRAENE-6,9,13-TRIONE
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	L7G	1	Ligand/Ion	(5R,8S,11S)-5-METHYL-8-(PROPAN-2-YL)-11-[(1E)-4-SULFANYLBUT-1-EN-1-YL]-3-THIA-7,10,14,17,21-PENTAAZATRICYCLO[14.3.1.1~2,5~]HENICOSA-1(20),2(21),16,18-TETRAENE-6,9,13-TRIONE
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	L7G	1	Ligand/Ion	(5R,8S,11S)-5-METHYL-8-(PROPAN-2-YL)-11-[(1E)-4-SULFANYLBUT-1-EN-1-YL]-3-THIA-7,10,14,17,21-PENTAAZATRICYCLO[14.3.1.1~2,5~]HENICOSA-1(20),2(21),16,18-TETRAENE-6,9,13-TRIONE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	K	-1	Ligand/Ion	POTASSIUM ION
2	L7G	2	Ligand/Ion	(5R,8S,11S)-5-METHYL-8-(PROPAN-2-YL)-11-[(1E)-4-SULFANYLBUT-1-EN-1-YL]-3-THIA-7,10,14,17,21-PENTAAZATRICYCLO[14.3.1.1~2,5~]HENICOSA-1(20),2(21),16,18-TETRAENE-6,9,13-TRIONE
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 , L7G 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 , HOH A:580 , HOH A:592	BINDING SITE FOR RESIDUE K A 403
4	AC4	SOFTWARE	HIS A:143 , PHE A:152 , HIS A:180 , PHE A:208 , TYR A:306 , ZN A:401 , HOH A:506 , LYS B:33 , TYR B:306	BINDING SITE FOR RESIDUE L7G A 404
5	AC5	SOFTWARE	ASP B:178 , HIS B:180 , ASP B:267 , L7G 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 , HOH B:501 , HOH B:505	BINDING SITE FOR RESIDUE K B 403
8	AC8	SOFTWARE	LYS A:33 , PRO A:273 , TYR A:306 , TYR B:100 , HIS B:143 , PHE B:152 , HIS B:180 , PHE B:208 , TYR B:306 , ZN B:401 , HOH B:512 , HOH B:582	BINDING SITE FOR RESIDUE L7G B 404

(no "SS Bond" information available for 4RN2)

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 4RN2)

(no "PROSITE Motif" information available for 4RN2)

(no "Exon" information available for 4RN2)

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:349
                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhhh......hhhhhhhhhhhhhhhhhhheee.....hhhhhh...hhhhhhhhhhhh.hhhhh...hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhh.....eeeee.....hhhhhhhh.....eeeeeeee................hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhh...eeeee................hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhh............hhhhhh................hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rn2 A  15 VPVYIYSPEYVSMCDSLAKIPKRADMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQSIEYGLTEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVV 377
                                    24        34        44        54        64        74        84|    ||108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368         
                                                                                                84|   98|                                                                                                                                                                                                                                                                                
                                                                                                 93   105

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...hhhhhhhhhhhhhh......hhhhh....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
                 4rn2 B  15 VPVYIYSPEYVSMCDSLAKIPKRADMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVV 377
                                    24        34        44        54        64        74        84 ||    100       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       
                                                                                                  86|                                                                                                                                                                                                                                                                                            
                                                                                                   93

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 4RN2)

(no "CATH Domain" information available for 4RN2)

(no "Pfam Domain" information available for 4RN2)

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

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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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