5FCW - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   HDAC8 COMPLEXED WITH A HYDROXAMIC ACID

Authors :   K. E. Cole, K. Perry

Date :   15 Dec 15 (Deposition) - 26 Oct 16 (Release) - 26 Oct 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.98

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

Keywords :   Histone Deacetylase, Hdac8, Hydroxamic Acid, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. A. Tabackman, R. Frankson, E. S. Marsan, K. Perry, K. E. Cole
Structure Of 'Linkerless' Hydroxamic Acid Inhibitor-Hdac8 Complex Confirms The Formation Of An Isoform-Specific Subpocket.
J. Struct. Biol. V. 195 373 2016
PubMed-ID: 27374062 | Reference-DOI: 10.1016/J.JSB.2016.06.023

Molecule 1 - HISTONE DEACETYLASE 8
	Chains	:	A, B
	EC Number	:	3.5.1.98
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	HDAC8, HDACL1, CDA07
	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 (5, 10)

No.	Name	Count	Type	Full Name
1	5YA	4	Ligand/Ion	4-NAPHTHALEN-1-YL-~{N}-OXIDANYL-BENZAMIDE
2	GOL	1	Ligand/Ion	GLYCEROL
3	K	2	Ligand/Ion	POTASSIUM ION
4	P6G	1	Ligand/Ion	HEXAETHYLENE GLYCOL
5	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	5YA	1	Ligand/Ion	4-NAPHTHALEN-1-YL-~{N}-OXIDANYL-BENZAMIDE
2	GOL	-1	Ligand/Ion	GLYCEROL
3	K	-1	Ligand/Ion	POTASSIUM ION
4	P6G	1	Ligand/Ion	HEXAETHYLENE GLYCOL
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	5YA	3	Ligand/Ion	4-NAPHTHALEN-1-YL-~{N}-OXIDANYL-BENZAMIDE
2	GOL	1	Ligand/Ion	GLYCEROL
3	K	-1	Ligand/Ion	POTASSIUM ION
4	P6G	-1	Ligand/Ion	HEXAETHYLENE GLYCOL
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:101 , HIS A:142 , HIS A:143 , ASP A:178 , HIS A:180 , PHE A:208 , ASP A:267 , TYR A:306 , ZN A:402 , HOH A:655 , PRO B:273 , 5YA B:405	binding site for residue 5YA A 401
02	AC2	SOFTWARE	ASP A:178 , HIS A:180 , ASP A:267 , 5YA A:401	binding site for residue ZN A 402
03	AC3	SOFTWARE	ASP A:176 , ASP A:178 , HIS A:180 , SER A:199 , LEU A:200	binding site for residue K A 403
04	AC4	SOFTWARE	GLU A:170	binding site for residue P6G A 404
05	AC5	SOFTWARE	PRO A:273 , TYR B:100 , HIS B:143 , GLY B:151 , PHE B:152 , HIS B:180 , PHE B:208 , ASP B:267 , GLY B:304 , TYR B:306 , ZN B:402 , 5YA B:404 , HOH B:501	binding site for residue 5YA B 401
06	AC6	SOFTWARE	ASP B:178 , HIS B:180 , ASP B:267 , 5YA B:401 , HOH B:501	binding site for residue ZN B 402
07	AC7	SOFTWARE	ASP B:176 , ASP B:178 , HIS B:180 , SER B:199 , LEU B:200	binding site for residue K B 403
08	AC8	SOFTWARE	LYS A:33 , PRO A:273 , LYS B:33 , TYR B:100 , PRO B:273 , MET B:274 , 5YA B:401 , 5YA B:405	binding site for residue 5YA B 404
09	AC9	SOFTWARE	TYR A:100 , PHE A:152 , 5YA A:401 , ALA B:32 , LYS B:33 , PHE B:152 , TYR B:306 , 5YA B:404	binding site for residue 5YA B 405
10	AD1	SOFTWARE	ALA B:188 , HOH B:517 , HOH B:535	binding site for residue GOL B 406

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

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 5FCW)

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

(no "Exon" information available for 5FCW)

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.hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhheee.....hhhhhh...hhhhhhhhhhhhhh......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
                 5fcw A  13 SLVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDDHPDSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVV 377
                                    22        32        42        52        62        72        82    ||  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    
                                                                                                     87|                                                                                                                                                                                                                                                                                                
                                                                                                      89

Chain B from PDB  Type:PROTEIN  Length:353
                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhhhhhhh.....hhhhhhhhhhhhh.hhhhheee.....hhhhhh...hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhh.....eeeee.....hhhhhhhhh....eeeeeeee................hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee................hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhh...........hhhhhh................hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fcw B  14 LVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVV 377
                                    23        33        43        53        63        73        83||     104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374   
                                                                                                 84|                                                                                                                                                                                                                                                                                         
                                                                                                  96

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 5FCW)

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		5YA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		K	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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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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	5fcw
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	3.5.1.98
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(no "Related Entries Specified in the PDB File" available for 5FCW)

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (5, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (26, 26)

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