3U16 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   STRUCTURE OF BASE N-TERMINAL DOMAIN FROM ACINETOBACTER BAUMANNII BOUND TO 6-(P-BENZYLOXY)PHENYL-1-(PYRIDIN-4-YLMETHYL)-1H-PYRAZOLO[3,4-B]PYRIDINE-4-CARBOXYLIC ACID.

Authors :   A. M. Gulick, E. J. Drake, C. C. Aldrich, J. Neres

Date :   29 Sep 11 (Deposition) - 03 Oct 12 (Release) - 03 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Anl Superfamily, Adenylating Enzyme, 2, 3-Dihydroxybenzoate:Aryl Carrier Protein Ligase, Basf, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Neres, E. Drake, A. M. Gulick, C. C. Aldrich
Structure-Activity Relationship Of Base
To Be Published
PubMed: search

Molecule 1 - PEPTIDE ARYLATION ENZYME
	Chains	:	A, B
	EC Number	:	6.2.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PET15BTEV
	Gene	:	ACICU_02578, BASE
	Mutation	:	YES
	Organism Scientific	:	ACINETOBACTER BAUMANNII
	Organism Taxid	:	405416
	Strain	:	AB900

		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 (4, 10)

No.	Name	Count	Type	Full Name
1	CA	6	Ligand/Ion	CALCIUM ION
2	H89	2	Ligand/Ion	6-[4-(BENZYLOXY)PHENYL]-1-(PYRIDIN-4-YLMETHYL)-1H-PYRAZOLO[3,4-B]PYRIDINE-4-CARBOXYLIC ACID
3	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
4	MRD	1	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	H89	1	Ligand/Ion	6-[4-(BENZYLOXY)PHENYL]-1-(PYRIDIN-4-YLMETHYL)-1H-PYRAZOLO[3,4-B]PYRIDINE-4-CARBOXYLIC ACID
3	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
4	MRD	-1	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	H89	1	Ligand/Ion	6-[4-(BENZYLOXY)PHENYL]-1-(PYRIDIN-4-YLMETHYL)-1H-PYRAZOLO[3,4-B]PYRIDINE-4-CARBOXYLIC ACID
3	MPD	-1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
4	MRD	1	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL

Biological Unit 3 (3, 4)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	H89	2	Ligand/Ion	6-[4-(BENZYLOXY)PHENYL]-1-(PYRIDIN-4-YLMETHYL)-1H-PYRAZOLO[3,4-B]PYRIDINE-4-CARBOXYLIC ACID
3	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
4	MRD	1	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PRO A:238 , HIS A:241 , ASN A:242 , PHE A:243 , SER A:247 , PRO A:266 , GLY A:314 , PHE A:337 , GLY A:338 , MET A:339	BINDING SITE FOR RESIDUE H89 A 543
02	AC2	SOFTWARE	GLN A:53 , GLU A:58 , HOH A:784 , HOH A:785 , HOH A:794 , ASP B:171	BINDING SITE FOR RESIDUE CA A 544
03	AC3	SOFTWARE	GLN A:305 , LEU A:307 , ASN A:330 , HOH A:780 , HOH A:781 , ASP B:302	BINDING SITE FOR RESIDUE CA A 545
04	AC4	SOFTWARE	GLU A:327 , ASN A:330 , HOH A:619 , HOH A:620 , HOH A:782 , GLN B:279	BINDING SITE FOR RESIDUE CA A 546
05	AC5	SOFTWARE	SER A:418 , HOH A:575 , HOH A:576 , HOH A:577 , HOH A:647	BINDING SITE FOR RESIDUE CA A 547
06	AC6	SOFTWARE	CYS A:225 , GLY A:226 , THR A:231 , ASN A:281 , MET A:282 , LEU A:349	BINDING SITE FOR RESIDUE MPD A 548
07	AC7	SOFTWARE	PRO B:238 , HIS B:241 , ASN B:242 , PHE B:243 , SER B:247 , PRO B:266 , GLY B:314 , GLY B:338 , MET B:339 , ARG B:435	BINDING SITE FOR RESIDUE H89 B 543
08	AC8	SOFTWARE	SER B:418 , HOH B:562 , HOH B:563 , HOH B:591 , HOH B:654 , HOH B:795	BINDING SITE FOR RESIDUE CA B 544
09	AC9	SOFTWARE	GLN B:305 , LEU B:307 , ASN B:330 , HOH B:566 , HOH B:567 , HOH B:568 , HOH B:569	BINDING SITE FOR RESIDUE CA B 545
10	BC1	SOFTWARE	GLY B:226 , LEU B:227 , THR B:231 , ASN B:281 , MET B:282 , HOH B:770 , HOH B:781	BINDING SITE FOR RESIDUE MRD B 546

(no "SS Bond" information available for 3U16)

Asymmetric Unit

No.	Residues
1	Ser A:247	-	Pro A:248
2	Ser B:247	-	Pro B:248

(no "SAP(SNP)/Variant" information available for 3U16)

(no "PROSITE Motif" information available for 3U16)

(no "Exon" information available for 3U16)

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:433
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d3u16a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhh........hhhhhhhhhhh...eeeee..eeeehhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhh..eeeee..hhhhh.hhhhhhhhh......eeeee......eehhhhhhh...............eeeeee.......eeeeehhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhh..eeeehhhhhhhhhhhhh.hhhhhh...eeeee....hhhhhhhhhhhh..eeeeeee.....eee.....hhhhhhhh..ee.....eeeee............eeeeee..........hhhhhhhhh.....eeeeeeeee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u16 A   3 KQLIEFVRWSPERAQHYRNKGYWIDQPLTRILTVGVQSHPHSLAIICGERQLSYIELDRLSTNLATRLAEKGLGKGDTALVQLPNVAEFYIVFFALLKAGVVVLNALYSHRQYELNAFIKQIQPKLLIGSRQHEVFSNNQFIDSLHDVNLSPEIILMLNHQATDFGLLDWIETPAETFVDFSSTPADEVAFFQLSGTGTPKLIPRTHNDYDYSVRASAEICGLNSNTRLLCALPAPHNFMLSSPGALGVLHAGGCVVMAPNPEPLNCFSIIQRHQVNMASLVPSAVIMWLEKAAQYKDQIQSLKLLQVGGASFPESLARQVPEVLNCKLQQVFGMAEGLVNYTRLDDSDEQIFTTQGRPISSDDEIKIVDEQYREVPEGEIGMLATRGPYTFCGYYQSPEHNSQVFDEDNYYYSGDLVQRTPDGNLRVVGRIK 437
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192     ||204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434   
                                                                                                                                                                                                                             198|                                                                                                                                                                                                                                            
                                                                                                                                                                                                                              201

Chain B from PDB  Type:PROTEIN  Length:437
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d3u16b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhh........hhhhhhhhhhh...eeeee..eeeehhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhh..eeeee..hhhhh.hhhhhhhhhh.....eeeee......eehhhhhhh...............eeeeee.........eeeeehhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhh..eeeehhhhhhhhhhhhh.hhhhhh...eeeee....hhhhhhhhhhhh..eeeeeee.....eee.....hhhhhhhh..ee.....eeeee............eeeeee..........hhhhhhhhh.....eeeeeeeee.....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u16 B   3 KQLIEFVRWSPERAQHYRNKGYWIDQPLTRILTVGVQSHPHSLAIICGERQLSYIELDRLSTNLATRLAEKGLGKGDTALVQLPNVAEFYIVFFALLKAGVVVLNALYSHRQYELNAFIKQIQPKLLIGSRQHEVFSNNQFIDSLHDVNLSPEIILMLNHQATDFGLLDWIETPAETFVDFSSTPADEVAFFQLSGGSTGTPKLIPRTHNDYDYSVRASAEICGLNSNTRLLCALPAPHNFMLSSPGALGVLHAGGCVVMAPNPEPLNCFSIIQRHQVNMASLVPSAVIMWLEKAAQYKDQIQSLKLLQVGGASFPESLARQVPEVLNCKLQQVFGMAEGLVNYTRLDDSDEQIFTTQGRPISSDDEIKIVDEQYREVPEGEIGMLATRGPYTFCGYYQSPEHNSQVFDEDNYYYSGDLVQRTPDGNLRVVGRIKDQ 439
                                    12        22        32        42        52        62        72        82        92       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       382       392       402       412       422       432

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: Multi-domain proteins (alpha and beta) (2421)

Fold: Acetyl-CoA synthetase-like (64)

Superfamily: Acetyl-CoA synthetase-like (64)

Family: automated matches (26)

Protein domain: automated matches (26)

Acinetobacter baumannii [TaxId: 557601] (5)

1a	d3u16a_	A:
1b	d3u16b_	B:

(no "CATH Domain" information available for 3U16)

(no "Pfam Domain" information available for 3U16)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 3U16)

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
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		H89	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MPD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MRD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ser A:247 - Pro A:248	[ RasMol ]
		Ser B:247 - Pro B:248	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ 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 \| Biol. Unit 2 PNG format \| Biol. Unit 3 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
	3u16
		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
	(no 'UniProt ID/Accession number' available) \|
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProt

Access by Enzyme Classificator (EC Number)
	6.2.1.-
		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
	(no 'UniProt ID/Accession number' available) \|
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT

(no "Entries Sharing at Least One Protein Chain" available for 3U16)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (0, 0)

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