4A9V - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   PSEUDOMONAS FLUORESCENS PHOX

Authors :   S. C. Yong, P. Roversi, J. E. D. Lillington, O. B. Zeldin, E. F. Garman, S. B. C. Berks

Date :   28 Nov 11 (Deposition) - 05 Dec 12 (Release) - 17 Sep 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.10

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)

Keywords :   Hydrolase, Beta-Propeller (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. C. Yong, P. Roversi, J. Lillington, F. Rodriguez, M. Krehenbrink, O. B. Zeldin, E. F. Garman, S. M. Lea, B. C. Berks
A Complex Iron-Calcium Cofactor Catalyzing Phosphotransfer Chemistry
Science V. 345 1170 2014
PubMed-ID: 25190793 | Reference-DOI: 10.1126/SCIENCE.1254237

Molecule 1 - PHOX
	Atcc	:	13525
	Chains	:	A
	EC Number	:	3.1.3.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE60-PHOX AND PREP4
	Expression System Strain	:	C43 DELTA TAT
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 48-633
	Organism Scientific	:	PSEUDOMONAS FLUORESCENS
	Organism Taxid	:	205922
	Strain	:	PF0-1
	Synonym	:	ALKALINE PHOSPHATASE

		1
Asymmetric Unit	:	A
Biological Unit 1 (1x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 18)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	CL	1	Ligand/Ion	CHLORIDE ION
3	EDO	9	Ligand/Ion	1,2-ETHANEDIOL
4	FEO	1	Ligand/Ion	MU-OXO-DIIRON
5	LI	3	Ligand/Ion	LITHIUM ION
6	NA	2	Ligand/Ion	SODIUM ION

Biological Unit 1 (2, 10)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	EDO	9	Ligand/Ion	1,2-ETHANEDIOL
4	FEO	1	Ligand/Ion	MU-OXO-DIIRON
5	LI	-1	Ligand/Ion	LITHIUM ION
6	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:328 , ASP A:330 , GLN A:344 , HOH A:2297 , HOH A:2301	BINDING SITE FOR RESIDUE CL A 611
02	AC2	SOFTWARE	GLU A:279 , HOH A:2557 , HOH A:2560	BINDING SITE FOR RESIDUE LI A 612
03	AC3	SOFTWARE	ASP A:69 , CYS A:179 , THR A:534 , CA A:1591 , FEO A:1594 , HOH A:2185 , HOH A:2186 , HOH A:2806	BINDING SITE FOR RESIDUE LI A 613
04	AC4	SOFTWARE	GLY A:530 , GLY A:553 , ASN A:555 , GLY A:556 , GLY A:557 , HOH A:2867	BINDING SITE FOR RESIDUE NA A 614
05	AC5	SOFTWARE	ARG A:126 , PRO A:540 , ASP A:541 , HOH A:2221	BINDING SITE FOR RESIDUE NA A 615
06	AC6	SOFTWARE	ASP A:494 , GLU A:532 , HOH A:2245 , HOH A:2821 , HOH A:2822 , HOH A:2823 , HOH A:2866	BINDING SITE FOR RESIDUE LI A 616
07	AC7	SOFTWARE	PRO A:154 , HIS A:321 , GLY A:322 , GLN A:364 , LEU A:368 , HOH A:2547 , HOH A:2626 , HOH A:2628	BINDING SITE FOR RESIDUE EDO A 901
08	AC8	SOFTWARE	PRO A:99 , HIS A:100 , SER A:456 , PRO A:471 , HOH A:2145 , HOH A:2275 , HOH A:2894 , HOH A:2895	BINDING SITE FOR RESIDUE EDO A 903
09	AC9	SOFTWARE	PRO A:51 , ARG A:95 , TYR A:96 , TYR A:98 , PRO A:99 , LYS A:568 , HOH A:2139 , HOH A:2896	BINDING SITE FOR RESIDUE EDO A 904
10	BC1	SOFTWARE	PRO A:148 , GLN A:208 , PHE A:209 , LYS A:214 , HOH A:2381 , HOH A:2474 , HOH A:2480	BINDING SITE FOR RESIDUE EDO A 905
11	BC2	SOFTWARE	PRO A:77 , GLY A:187 , PHE A:255 , EDO A:909 , HOH A:2196 , HOH A:2440 , HOH A:2450 , HOH A:2900 , HOH A:2901	BINDING SITE FOR RESIDUE EDO A 906
12	BC3	SOFTWARE	THR A:188 , GLU A:251 , ASP A:253 , ARG A:264 , HOH A:2543	BINDING SITE FOR RESIDUE EDO A 907
13	BC4	SOFTWARE	SER A:52 , HOH A:2134 , HOH A:2135 , HOH A:2902	BINDING SITE FOR RESIDUE EDO A 908
14	BC5	SOFTWARE	LEU A:73 , PHE A:74 , GLU A:75 , LYS A:183 , EDO A:906 , HOH A:2196 , HOH A:2437 , HOH A:2440	BINDING SITE FOR RESIDUE EDO A 909
15	BC6	SOFTWARE	SER A:152 , GLY A:153 , ASP A:320 , HOH A:2388 , HOH A:2389 , HOH A:2625	BINDING SITE FOR RESIDUE EDO A 910
16	BC7	SOFTWARE	GLU A:273 , GLU A:387 , ASP A:479 , LI A:613 , CA A:1592 , FEO A:1594 , HOH A:2185 , HOH A:2186 , HOH A:2706 , HOH A:2806	BINDING SITE FOR RESIDUE CA A1591
17	BC8	SOFTWARE	GLU A:387 , ASP A:479 , ASP A:494 , CA A:1591 , HOH A:2704 , HOH A:2705 , HOH A:2706	BINDING SITE FOR RESIDUE CA A1592
18	BC9	SOFTWARE	GLU A:90 , CYS A:179 , GLU A:194 , GLU A:273 , ASP A:292 , GLU A:387 , LI A:613 , CA A:1591 , HOH A:2186 , HOH A:2239 , HOH A:2453 , HOH A:2706	BINDING SITE FOR RESIDUE FEO A1594

(no "SS Bond" information available for 4A9V)

Asymmetric Unit

No.	Residues
1	Phe A:560	-	Pro A:561

(no "SAP(SNP)/Variant" information available for 4A9V)

(no "PROSITE Motif" information available for 4A9V)

(no "Exon" information available for 4A9V)

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:581
 aligned with Q3K5N8_PSEPF | Q3K5N8 from UniProtKB/TrEMBL  Length:633

    Alignment length:581
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            633  
                                    64        74        84        94       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       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624        |- 
         Q3K5N8_PSEPF    55 SRLLGFDSIPAATTDTISLPKGYKSSVLISWGQPLHKNGPAFDPSGNGTAAAQEVQFGDNNDGMSLFEFPGEKNRALMAINNEYTNYRYLYPHGGMPQSAEDVRKALACEGVSVIEVQRKNGQWQFVQGSRYNRRIHGNSPLRISGPAAGHELMKTSADKHGKKVLGTFQNCANGKTPWGTYLTCEENFTDCFGSSNAQQQFDPAQKRYGVSAASREINWHPFDPRFDMAKNPNELNRHGWVVEIDPFDPQSTPVKRTALGRFKHENAALAETDDGRAVVYMGDDERGEFIYKFVSRDKINHRNAKANRDILDHGTLYVARFDAGDGNPDHPKGQGQWIELTHGKNGIDASSGFADQAEVLIHARLAASVVGATRMDRPEWIVVSPKDGQVYCTLTNNAKRGEDGQPVGGPNPREKNVYGQILRWRTDRDDHASKTFAWDLFVVAGNPSVHAGTPKGGSSNITPQNMFNSPDGLGFDKAGRLWILTDGDSSNAGDFAGMGNNQMLCADPATGEIRRFMVGPIGCEVTGISFSPDQKTLFVGIQHPGENGGSTFPEHLPNGKPRSSVMAITREDGGIVGA--   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................eeeeeeee..................hhhhhh......eeeeeeeee..eeeeeeeeeee...hhhhhh.......hhhhhhhhhhh.eeeeeeeeee..eeee.......eeee...eeeee.....hhhhh........eee....eeeeee.....eeeee.hhhhhh.........hhhhhhhh.............hhhh....hhhhhhhh..eeee.........eee.hhh.......eeee....eeeeeee.......eeeeeeeee....hhhhhhhhhh.eeeeeeee..........eeeeeeee........hhhhh..hhhhhhhhhhhhhhhh.......eeeeee......eeeee.........................eeeeeee.hhh....eeeeeeeee.........hhhhh............eeeeee.....eeeee......hhhhh.....eeeee......eeeeee.....eeeeeee.....eeeeeee.....................eeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a9v A   8 SRLLGFDSIPAATTDTISLPKGYKSSVLISWGQPLHKNGPAFDPSGNGTAAAQEVQFGDNNDGMSLFEFPGEKNRALMAINNEYTNYRYLYPHGGMPQSAEDVRKALACEGVSVIEVQRKNGQWQFVQGSRYNRRIHGNSPLRISGPAAGHELMKTSADKHGKKVLGTFQNCANGKTPWGTYLTCEENFTDCFGSSNAQQQFDPAQKRYGVSAASREINWHPFDPRFDMAKNPNELNRHGWVVEIDPFDPQSTPVKRTALGRFKHENAALAETDDGRAVVYMGDDERGEFIYKFVSRDKINHRNAKANRDILDHGTLYVARFDAGDGNPDHPKGQGQWIELTHGKNGIDASSGFADQAEVLIHARLAASVVGATRMDRPEWIVVSPKDGQVYCTLTNNAKRGEDGQPVGGPNPREKNVYGQILRWRTDRDDHASKTFAWDLFVVAGNPSVHAGTPKGGSSNITPQNMFNSPDGLGFDKAGRLWILTDGDSSNAGDFAGMGNNQMLCADPATGEIRRFMVGPIGCEVTGISFSPDQKTLFVGIQHPGENGGSTFPEHLPNGKPRSSVMAITREDGGIVGAHH 588
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587

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 4A9V)

(no "CATH Domain" information available for 4A9V)

(no "Pfam Domain" information available for 4A9V)

Asymmetric Unit(hide GO term definitions)

Chain A (Q3K5N8_PSEPF | Q3K5N8)

molecular function
	GO:0046872		metal ion binding		Interacting selectively and non-covalently with any metal ion.
	GO:0000166		nucleotide binding		Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

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 ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FEO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		LI	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ 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 ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]
		BC8	[ RasMol ]	+environment [ RasMol ]
		BC9	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Phe A:560 - Pro A:561	[ RasMol ]

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
	4a9v
		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
	Q3K5N8_PSEPF \| Q3K5N8
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	3.1.3.1
		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
	Q3K5N8_PSEPF \| Q3K5N8
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	Q3K5N8_PSEPF \| Q3K5N8	:	3zwu 4a9x 4alf 4amf

3zwu	PSEUDOMONAS FLUORESCENS PHOX IN COMPLEX WITH VANADATE, A TRANSITION STATE ANALOGUE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 18)

Sites (18, 18)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (2, 2)

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