4QA6 - JenaLib

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Title :   CRYSTAL STRUCTURE OF I243N/Y306F HDAC8 IN COMPLEX WITH A TETRAPEPTIDE SUBSTRATE

Authors :   C. Decroos, C. B. Bowman, J. -A. S. Moser, K. E. Christianson, M. A. Deard D. W. Christianson

Date :   02 May 14 (Deposition) - 06 Aug 14 (Release) - 01 Oct 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

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

Keywords :   Metalloenzyme, Hydrolase, Histone Deacetylase, Enzyme Substrate Complex, Cornelia De Lange Syndrome, Arginase/Deacetylase Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Decroos, C. M. Bowman, J. A. Moser, K. E. Christianson, M. A. Deardorff, D. W. Christianson
Compromised Structure And Function Of Hdac8 Mutants Identified In Cornelia De Lange Syndrome Spectrum Disorders
Acs Chem. Biol. V. 9 2157 2014
PubMed-ID: 25075551 | Reference-DOI: 10.1021/CB5003762

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

Molecule 2 - TETRAPEPTIDE SUBSTRATE
	Chains	:	C, D
	Engineered	:	YES
	Other Details	:	SYNTHETIC PEPTIDE
	Synthetic	:	YES

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 16)

No.	Name	Count	Type	Full Name
1	ACE	2	Mod. Amino Acid	ACETYL GROUP
2	ALY	4	Mod. Amino Acid	N(6)-ACETYLLYSINE
3	GOL	2	Ligand/Ion	GLYCEROL
4	K	4	Ligand/Ion	POTASSIUM ION
5	MCM	2	Ligand/Ion	7-AMINO-4-METHYL-CHROMEN-2-ONE
6	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (4, 5)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP
2	ALY	2	Mod. Amino Acid	N(6)-ACETYLLYSINE
3	GOL	1	Ligand/Ion	GLYCEROL
4	K	-1	Ligand/Ion	POTASSIUM ION
5	MCM	1	Ligand/Ion	7-AMINO-4-METHYL-CHROMEN-2-ONE
6	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (4, 5)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP
2	ALY	2	Mod. Amino Acid	N(6)-ACETYLLYSINE
3	GOL	1	Ligand/Ion	GLYCEROL
4	K	-1	Ligand/Ion	POTASSIUM ION
5	MCM	1	Ligand/Ion	7-AMINO-4-METHYL-CHROMEN-2-ONE
6	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:178 , HIS A:180 , ASP A:267 , HOH A:642 , ALY C:505	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:535 , HOH A:536	BINDING SITE FOR RESIDUE K A 403
04	AC4	SOFTWARE	GLU A:65 , ARG A:164 , ARG A:167 , HOH A:586	BINDING SITE FOR RESIDUE GOL A 404
05	AC5	SOFTWARE	ASP B:178 , HIS B:180 , ASP B:267 , HOH B:629 , ALY D:505	BINDING SITE FOR RESIDUE ZN B 401
06	AC6	SOFTWARE	ASP B:176 , ASP B:178 , HIS B:180 , SER B:199 , LEU B:200	BINDING SITE FOR RESIDUE K B 402
07	AC7	SOFTWARE	PHE B:189 , THR B:192 , VAL B:195 , TYR B:225 , HOH B:509 , HOH B:513	BINDING SITE FOR RESIDUE K B 403
08	AC8	SOFTWARE	LYS A:33 , TYR A:100 , ASP A:101 , PHE A:152 , PRO B:273 , ALY C:504 , ALY C:505 , MCM D:601 , HOH D:709	BINDING SITE FOR RESIDUE MCM C 601
09	AC9	SOFTWARE	PRO A:273 , LYS B:33 , TYR B:100 , ASP B:101 , PHE B:152 , MCM C:601 , ALY D:504 , ALY D:505 , HOH D:709	BINDING SITE FOR RESIDUE MCM D 601
10	BC1	SOFTWARE	PHE B:208 , ACE D:501 , ARG D:502 , HIS D:503 , HOH D:701	BINDING SITE FOR RESIDUE GOL D 602

(no "SS Bond" information available for 4QA6)

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 4QA6)

(no "PROSITE Motif" information available for 4QA6)

(no "Exon" information available for 4QA6)

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...hhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhh.....eeeee.....hhhhhhhh.....eeeeeeee................hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh..........hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhh............hhhhhh................hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qa6 A  14 LVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQNCESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGFNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVV 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:364
                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhhhhhh......hhhhhhhhhhhhhhhhhhheee.....hhhhhh...hhhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhh.....eeeee.....hhhhhhhh.....eeeeeeee................hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee................hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhh............hhhhhh................hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qa6 B  14 LVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQNCESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGFNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVV 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 C from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 4qa6 C 501 xRHkk 505
                            |  ||
                          501-ACE
                             504-ALY
                              505-ALY

Chain D from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 4qa6 D 501 xRHkk 505
                            |  ||
                            |  ||
                          501-ACE
                             504-ALY
                              505-ALY

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 4QA6)

(no "CATH Domain" information available for 4QA6)

(no "Pfam Domain" information available for 4QA6)

Asymmetric Unit(hide GO term definitions)

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	Ligands, Modified Residues, Ions
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		K	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Sites
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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 (6, 16)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

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Gene Ontology (26, 26)

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