2Q4V - JenaLib

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   ENSEMBLE REFINEMENT OF THE PROTEIN CRYSTAL STRUCTURE OF THIALYSINE N-ACETYLTRANSFERASE (SSAT2) FROM HOMO SAPIENS

Authors :   E. J. Levin, D. A. Kondrashov, G. E. Wesenberg, G. N. Phillips Jr. , Cent Eukaryotic Structural Genomics (Cesg)

Date :   31 May 07 (Deposition) - 19 Jun 07 (Release) - 10 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.84

Chains :   Asym. Unit : A,B  (8x)
Biol. Unit 1: A,B  (1x)

Keywords :   Ensemble Refinement, Refinement Methodology Development, Ssat2, Bc011751, Aah11751, Thialysine N-Acetyltransferase, Structural Genomics, Protein Structure Initiative, Psi, Center For Eukaryotic Structural Genomics, Cesg, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. J. Levin, D. A. Kondrashov, G. E. Wesenberg, G. N. Phillips
Ensemble Refinement Of Protein Crystal Structures: Validation And Application.
Structure V. 15 1040 2007
PubMed-ID: 17850744 | Reference-DOI: 10.1016/J.STR.2007.06.019
(for further references see the PDB file header)

Molecule 1 - DIAMINE ACETYLTRANSFERASE 2
	Chains	:	A, B
	EC Number	:	2.3.1.57
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PVP16
	Expression System Strain	:	B834 P(RARE2)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	SAT2, SSAT2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SPERMIDINE/SPERMINE N(1)-ACETYLTRANSFERASE 2, POLYAMINE N- ACETYLTRANSFERASE 2

		1	2
Asymmetric Unit (8x)	:	A	B
Biological Unit 1 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	ACO	1	Ligand/Ion	ACETYL COENZYME *A
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 5)

No.	Name	Count	Type	Full Name
1	ACO	1	Ligand/Ion	ACETYL COENZYME *A
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:24 , PHE A:27 , LEU A:91 , GLU A:92 , ASP A:93 , ILE A:94 , TYR A:95 , VAL A:96 , ARG A:101 , GLY A:102 , GLN A:103 , GLY A:104 , GLY A:106 , SER A:107 , LEU A:127 , ALA A:128 , ASN A:133 , ARG A:135 , LEU A:139 , TYR A:140 , HOH A:311 , HOH A:314 , HOH A:320 , HOH A:364 , ARG B:101 , GLY B:102 , ARG B:135 , HOH B:190 , HOH B:322	BINDING SITE FOR RESIDUE ACO A 306

(no "SS Bond" information available for 2Q4V)

(no "Cis Peptide Bond" information available for 2Q4V)

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_020465	R	126	C	SAT2_HUMAN	Polymorphism	13894	A/B	R	126	C

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_020465	R	126	C	SAT2_HUMAN	Polymorphism	13894	A/B	R	126	C

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GNAT	PS51186	Gcn5-related N-acetyltransferase (GNAT) domain profile.	SAT2_HUMAN	4-168	2	A:4-168 B:4-168

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GNAT	PS51186	Gcn5-related N-acetyltransferase (GNAT) domain profile.	SAT2_HUMAN	4-168	2	A:4-168 B:4-168

Asymmetric Unit (6, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000269298	1b	ENSE00001061698	chr17:7531164-7530888	277	SAT2_HUMAN	1-22	22	2	A:3-22 B:2-22	20 21
1.2	ENST00000269298	2	ENSE00000949284	chr17:7530732-7530681	52	SAT2_HUMAN	23-40	18	2	A:23-40 (gaps) B:23-40	18 18
1.3	ENST00000269298	3	ENSE00000949285	chr17:7530544-7530461	84	SAT2_HUMAN	40-68	29	2	A:40-68 (gaps) B:40-59	29 20
1.4	ENST00000269298	4	ENSE00000949286	chr17:7530362-7530261	102	SAT2_HUMAN	68-102	35	2	A:68-102 B:70-102	35 33
1.5	ENST00000269298	5	ENSE00000949287	chr17:7530111-7530071	41	SAT2_HUMAN	102-115	14	2	A:102-115 B:102-115	14 14
1.6a	ENST00000269298	6a	ENSE00001556146	chr17:7529932-7529556	377	SAT2_HUMAN	116-170	55	2	A:116-169 B:116-170	54 55

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:156
 aligned with SAT2_HUMAN | Q96F10 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:167
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       
           SAT2_HUMAN     3 SVRIREAKEGDCGDILRLIRELAEFEKLSDQVKISEEALRADGFGDNPFYHCLVAEILPAPGKLLGPCVVGYGIYYFIYSTWKGRTIYLEDIYVMPEYRGQGIGSKIIKKVAEVALDKGCSQFRLAVLDWNQRAMDLYKALGAQDLTEAEGWHFFCFQGEATRKLAG 169
               SCOP domains d2q4va_ A: Diamine acetyltra    nsferase 2                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee....hhhhhhhhhhhhhhhhhhhh.----..hhhhhhhhhh......eeeeeee.-------..eeeeeeeeeeeee...eeeeeeeeeee.hhhh..hhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh..ee......eeeeeeehhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------C------------------------------------------- SAPs(SNPs)
                    PROSITE -GNAT  PDB: A:4-168 UniProt: 4-168                                                                                                                                    - PROSITE
           Transcript 1 (1) Exon 1.1b           Exon 1.2          ---------------------------Exon 1.4  PDB: A:68-102            -------------Exon 1.6a  PDB: A:116-169 UniProt: 116-170             Transcript 1 (1)
           Transcript 1 (2) -------------------------------------Exon 1.3  PDB: A:40-68 (gaps)---------------------------------Exon 1.5      ------------------------------------------------------ Transcript 1 (2)
                 2q4v A   3 SVRIREAKEGDCGDILRLIRELAEFEKL----KISEEALRADGFGDNPFYHCLVAEIL-------GPCVVGYGIYYFIYSTWKGRTIYLEDIYVmPEYRGQGIGSKIIKKVAEVALDKGCSQFRLAVLDWNQRAmDLYKALGAQDLTEAEGWHFFCFQGEATRKLAG 169
                                    12        22       | -  |     42        52       | -     |  72        82        92    |  102       112       122       132    |  142       152       162       
                                                      30   35                       60      68                           97-MSE                                 137-MSE

Chain B from PDB  Type:PROTEIN  Length:159
 aligned with SAT2_HUMAN | Q96F10 from UniProtKB/Swiss-Prot  Length:170

    Alignment length:169
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161         
           SAT2_HUMAN     2 ASVRIREAKEGDCGDILRLIRELAEFEKLSDQVKISEEALRADGFGDNPFYHCLVAEILPAPGKLLGPCVVGYGIYYFIYSTWKGRTIYLEDIYVMPEYRGQGIGSKIIKKVAEVALDKGCSQFRLAVLDWNQRAMDLYKALGAQDLTEAEGWHFFCFQGEATRKLAGK 170
               SCOP domains d2q4vb_ B: Diamine acetyltransferase 2                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------Acetyltransf_1-2q4vB01 B:70-146                                              ------------------------ Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------Acetyltransf_1-2q4vB02 B:70-146                                              ------------------------ Pfam domains (2)
         Sec.struct. author ...eeee.hhhhhhhhhhhhhhhhhhh.hhhhh..hhhhhhhhhhh.....eeeeee.----------...eeeeeeeee.....eeeeeeeeee.hhhh..hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhh...ee.......eeeeehhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------C-------------------------------------------- SAPs(SNPs)
                    PROSITE --GNAT  PDB: B:4-168 UniProt: 4-168                                                                                                                                    -- PROSITE
           Transcript 1 (1) Exon 1.1b  PDB: B:2-2Exon 1.2          ---------------------------Exon 1.4  PDB: B:70-102            -------------Exon 1.6a  PDB: B:116-170 UniProt: 116-170              Transcript 1 (1)
           Transcript 1 (2) --------------------------------------Exon 1.3  PDB: B:40-59       ---------------------------------Exon 1.5      ------------------------------------------------------- Transcript 1 (2)
                 2q4v B   2 ASVRIREAKEGDCGDILRLIRELAEFEKLSDQVKISEEALRADGFGDNPFYHCLVAEI----------CVVGYGIYYFIYSTWKGRTIYLEDIYVmPEYRGQGIGSKIIKKVAEVALDKGCSQFRLAVLDWNQRAmDLYKALGAQDLTEAEGWHFFCFQGEATRKLAGK 170
                                    11        21        31        41        51       | -        71        81        91     | 101       111       121       131     | 141       151       161         
                                                                                    59         70                         97-MSE                                 137-MSE

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Acyl-CoA N-acyltransferases (Nat) (250)

Superfamily: Acyl-CoA N-acyltransferases (Nat) (250)

Family: N-acetyl transferase, NAT (154)

Protein domain: Diamine acetyltransferase 2 (2)

Human (Homo sapiens) [TaxId: 9606] (2)

1a	d2q4va_	A:
1b	d2q4vb_	B:

(no "CATH Domain" information available for 2Q4V)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Acetyltrans (109)

Family: Acetyltransf_1 (58)

Homo sapiens (Human) (6)

1a	Acetyltransf_1-2q4vB01	B:70-146
1b	Acetyltransf_1-2q4vB02	B:70-146

Asymmetric Unit(hide GO term definitions)

Chain A,B (SAT2_HUMAN | Q96F10)

molecular function
	GO:0008080	N-acetyltransferase activity	Catalysis of the transfer of an acetyl group to a nitrogen atom on the acceptor molecule.
	GO:0004145	diamine N-acetyltransferase activity	Catalysis of the reaction: acetyl-CoA + an alkane-alpha,omega-diamine = CoA + an N-acetyldiamine.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0016746	transferase activity, transferring acyl groups	Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
	GO:0046204	nor-spermidine metabolic process	The chemical reactions and pathways involving nor-spermidine, a compound related to spermidine, N-(3-aminopropyl)-1,4-diaminobutane.
	GO:0032920	putrescine acetylation	The modification of putrescine by addition of acetyl groups.
	GO:0009447	putrescine catabolic process	The chemical reactions and pathways resulting in the breakdown of putrescine, 1,4-diaminobutane; putrescine is the metabolic precursor of spermidine and spermine.
	GO:0032918	spermidine acetylation	The modification of spermidine by addition of acetyl groups.
	GO:0032919	spermine acetylation	The modification of spermine by addition of acetyl groups.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		ACO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2q4v)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2q4v
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	SAT2_HUMAN \| Q96F10
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.3.1.57
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	SAT2_HUMAN \| Q96F10
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	SAT2_HUMAN \| Q96F10	:	2bei

2bei	ORIGINAL REFINEMENT BASED ON SAME DATA AND R-FREE SET.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

PROSITE Motifs (1, 2)

Exons (6, 12)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (11, 11)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File