4QA1 - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A188T HDAC8 IN COMPLEX WITH M344

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 :   1.92

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Metalloenzyme, Hydrolase, Histone Deacetylase, Enzyme Inhibitor 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, C, D
	EC Number	:	3.5.1.98
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PHD2-XA-HIS
	Expression System Strain	:	BL(21)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	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 20)

No.	Name	Count	Type	Full Name
1	B3N	4	Ligand/Ion	4-(DIMETHYLAMINO)-N-[7-(HYDROXYAMINO)-7-OXOHEPTYL]BENZAMIDE
2	GOL	4	Ligand/Ion	GLYCEROL
3	K	8	Ligand/Ion	POTASSIUM ION
4	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 2)

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

Biological Unit 2 (2, 3)

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

Biological Unit 3 (2, 2)

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

Biological Unit 4 (1, 1)

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

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:176 , ASP A:178 , HIS A:180 , SER A:199 , LEU A:200	BINDING SITE FOR RESIDUE K A 401
02	AC2	SOFTWARE	PHE A:189 , THR A:192 , VAL A:195 , TYR A:225 , HOH A:507 , HOH A:514	BINDING SITE FOR RESIDUE K A 402
03	AC3	SOFTWARE	ASP A:178 , HIS A:180 , ASP A:267 , B3N A:404	BINDING SITE FOR RESIDUE ZN A 403
04	AC4	SOFTWARE	TYR A:100 , ASP A:101 , HIS A:142 , HIS A:143 , GLY A:151 , PHE A:152 , ASP A:178 , HIS A:180 , ASP A:267 , TYR A:306 , ZN A:403 , GOL A:405 , HOH A:675 , PHE B:152 , PRO B:273 , MET B:274 , TYR B:306	BINDING SITE FOR RESIDUE B3N A 404
05	AC5	SOFTWARE	LYS A:33 , PHE A:152 , B3N A:404 , LYS B:33	BINDING SITE FOR RESIDUE GOL A 405
06	AC6	SOFTWARE	ASP B:176 , ASP B:178 , HIS B:180 , SER B:199 , LEU B:200	BINDING SITE FOR RESIDUE K B 401
07	AC7	SOFTWARE	PHE B:189 , THR B:192 , VAL B:195 , TYR B:225 , HOH B:501 , HOH B:504	BINDING SITE FOR RESIDUE K B 402
08	AC8	SOFTWARE	ASP B:178 , HIS B:180 , ASP B:267 , B3N B:404	BINDING SITE FOR RESIDUE ZN B 403
09	AC9	SOFTWARE	LYS A:33 , PRO A:273 , TYR A:306 , TYR B:100 , HIS B:142 , HIS B:143 , GLY B:151 , PHE B:152 , ASP B:178 , HIS B:180 , PHE B:208 , ASP B:267 , TYR B:306 , ZN B:403 , HOH B:512 , HOH B:696 , HOH B:783	BINDING SITE FOR RESIDUE B3N B 404
10	BC1	SOFTWARE	ALA B:68 , THR B:69 , PHE B:70 , HIS B:71 , THR B:72 , HOH B:576	BINDING SITE FOR RESIDUE GOL B 405
11	BC2	SOFTWARE	ALA A:32 , LYS A:33 , PRO A:103 , ALA B:32 , LYS B:33 , HOH B:659 , HOH B:771 , HOH B:841	BINDING SITE FOR RESIDUE GOL B 406
12	BC3	SOFTWARE	ASP C:176 , ASP C:178 , HIS C:180 , SER C:199 , LEU C:200	BINDING SITE FOR RESIDUE K C 401
13	BC4	SOFTWARE	PHE C:189 , THR C:192 , VAL C:195 , TYR C:225 , HOH C:521 , HOH C:527	BINDING SITE FOR RESIDUE K C 402
14	BC5	SOFTWARE	ASP C:178 , HIS C:180 , ASP C:267 , B3N C:404	BINDING SITE FOR RESIDUE ZN C 403
15	BC6	SOFTWARE	TYR C:100 , ASP C:101 , HIS C:142 , HIS C:143 , GLY C:151 , PHE C:152 , ASP C:178 , HIS C:180 , PHE C:208 , ASP C:267 , TYR C:306 , ZN C:403 , HOH C:658 , PHE D:152 , PRO D:273 , MET D:274 , TYR D:306	BINDING SITE FOR RESIDUE B3N C 404
16	BC7	SOFTWARE	ALA C:32 , LYS C:33 , PRO C:103 , ALA D:32 , LYS D:33	BINDING SITE FOR RESIDUE GOL C 405
17	BC8	SOFTWARE	ASP D:176 , ASP D:178 , HIS D:180 , SER D:199 , LEU D:200	BINDING SITE FOR RESIDUE K D 401
18	BC9	SOFTWARE	PHE D:189 , THR D:192 , VAL D:195 , TYR D:225 , HOH D:501 , HOH D:502	BINDING SITE FOR RESIDUE K D 402
19	CC1	SOFTWARE	ASP D:178 , HIS D:180 , ASP D:267 , B3N D:404	BINDING SITE FOR RESIDUE ZN D 403
20	CC2	SOFTWARE	LYS C:33 , PHE C:152 , PRO C:273 , TYR C:306 , TYR D:100 , HIS D:142 , HIS D:143 , GLY D:151 , ASP D:178 , HIS D:180 , PHE D:208 , ASP D:267 , GLY D:304 , TYR D:306 , ZN D:403 , HOH D:532 , HOH D:691	BINDING SITE FOR RESIDUE B3N D 404

(no "SS Bond" information available for 4QA1)

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
5	Phe C:208	-	Pro C:209
6	Gly C:341	-	Pro C:342
7	Phe D:208	-	Pro D:209
8	Gly D:341	-	Pro D:342

(no "SAP(SNP)/Variant" information available for 4QA1)

(no "PROSITE Motif" information available for 4QA1)

(no "Exon" information available for 4QA1)

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:354
                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee.hhhhhhhhh......hhhhhhhhhhhhhhhhhhheee.....hhhhhh...hhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhh.....eeeee.....hhhhhhhh.....eeeeeeee................hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh..........hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhh...........hhhhhh................hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4qa1 A  14 LVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDTFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHV 376
                                    23        33        43        53        63        73        83 ||    102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372    
                                                                                                  85|                                                                                                                                                                                                                                                                                         
                                                                                                   95

Chain B from PDB  Type:PROTEIN  Length:370
                                                                                                                                                                                                                                                                                                                                                                                                                  
               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.hhhhh..........hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhh............hhhhhh................hhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qa1 B  14 LVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDTFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVVIEGRGS 383
                                    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       383

Chain C from PDB  Type:PROTEIN  Length:353
                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhheee.....hhhhhh...hhhhhhhhhhhh.............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
                 4qa1 C  14 LVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDTFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHV 376
                                    23        33        43        53        63        73        83 ||    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   
                                                                                                  85|                                                                                                                                                                                                                                                                                        
                                                                                                   96

Chain D from PDB  Type:PROTEIN  Length:370
                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhhhhhh......hhhhhhhhhhhhhhhhhhheee.....hhhhhh...hhhhhhhhhhhhhhh......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
                 4qa1 D  14 LVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDTFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVVIEGRGS 383
                                    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       383

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 4QA1)

(no "CATH Domain" information available for 4QA1)

(no "Pfam Domain" information available for 4QA1)

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 ]
		Gly C:341 - Pro C:342	[ RasMol ]
		Gly D:341 - Pro D:342	[ RasMol ]
		Phe A:208 - Pro A:209	[ RasMol ]
		Phe B:208 - Pro B:209	[ RasMol ]
		Phe C:208 - Pro C:209	[ RasMol ]
		Phe D:208 - Pro D:209	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 20)

Sites (20, 20)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

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