2POX - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Title :   DARK STATE STRUCTURE OF THE REVERSIBLY SWITCHABLE FLUORESCENT PROTEIN DRONPA

Authors :   S. Trowitzsch, G. Weber, M. C. Wahl

Date :   27 Apr 07 (Deposition) - 17 Jul 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Luminescent Protein; Reversibly Switchable Fluorescent Protein; Green-Fluorescent Protein-Like Protein, Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Andresen, A. C. Stiel, S. Trowitzsch, G. Weber, C. Eggeling, M. C. Wahl, S. W. Hell, S. Jakobs
Structural Basis For Reversible Photoswitching In Dronpa
Proc. Natl. Acad. Sci. Usa V. 104 13005 2007
PubMed-ID: 17646653 | Reference-DOI: 10.1073/PNAS.0700629104

Molecule 1 - FLUORESCENT PROTEIN DRONPA
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRSETB-DRONPA
	Expression System Strain	:	HMS174(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DRONPA
	Organism Scientific	:	ECHINOPHYLLIA SP. SC22
	Organism Taxid	:	301887

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 4)

No.	Name	Count	Type	Full Name
1	GYC	4	Mod. Amino Acid	[(4Z)-2-[(1R)-1-AMINO-2-MERCAPTOETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID

(no "Site" information available for 2POX)

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

Asymmetric/Biological Unit

No.	Residues
1	Gly A:48	-	Pro A:49
2	Phe A:83	-	Pro A:84
3	Gly B:48	-	Pro B:49
4	Phe B:83	-	Pro B:84
5	Gly B:165	-	Gly B:166
6	Gly C:48	-	Pro C:49
7	Phe C:83	-	Pro C:84
8	Gly D:48	-	Pro D:49
9	Phe D:83	-	Pro D:84

(no "SAP(SNP)/Variant" information available for 2POX)

(no "PROSITE Motif" information available for 2POX)

(no "Exon" information available for 2POX)

Asymmetric/Biological 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:219
 aligned with Q5TLG6_9CNID | Q5TLG6 from UniProtKB/TrEMBL  Length:224

    Alignment length:221
                               1                                                                                                                                                                                                                         
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217 
         Q5TLG6_9CNID     - ---MSVIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTTVFCYGNRVFAKYPENIVDYFKQSFPEGYSWERSMNYEDGGICNATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWEPSTEKLYVRDGVLKGDVNMALSLEGGGHYRCDFKTTYKAKKVVQLPDYHFVDHHIEIKSHDKDYSNVNLHEHAEAHSE 218
               SCOP domains d2poxa_ A: automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh...eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee.......hhhhhh...--............hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pox A  -2 KDPMSVIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTTVFc--NRVFAKYPENIVDYFKQSFPEGYSWERSMNYEDGGICNATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWEPSTEKLYVRDGVLKGDVNMALSLEGGGHYRCDFKTTYKAKKVVQLPDYHFVDHHIEIKSHDKDYSNVNLHEHAEAHSE 218
                                     7        17        27        37        47        57    |  |67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217 
                                                                                           62-GYC

Chain B from PDB  Type:PROTEIN  Length:220
 aligned with Q5TLG6_9CNID | Q5TLG6 from UniProtKB/TrEMBL  Length:224

    Alignment length:222
                               1                                                                                                                                                                                                                          
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217  
         Q5TLG6_9CNID     - ---MSVIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTTVFCYGNRVFAKYPENIVDYFKQSFPEGYSWERSMNYEDGGICNATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWEPSTEKLYVRDGVLKGDVNMALSLEGGGHYRCDFKTTYKAKKVVQLPDYHFVDHHIEIKSHDKDYSNVNLHEHAEAHSEL 219
               SCOP domains d2poxb_ B: automated matches                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh....eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee.......hhhhhh...--............hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2pox B  -2 KDPMSVIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTTVFc--NRVFAKYPENIVDYFKQSFPEGYSWERSMNYEDGGICNATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWEPSTEKLYVRDGVLKGDVNMALSLEGGGHYRCDFKTTYKAKKVVQLPDYHFVDHHIEIKSHDKDYSNVNLHEHAEAHSEL 219
                                     7        17        27        37        47        57    |  |67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217  
                                                                                           62-GYC

Chain C from PDB  Type:PROTEIN  Length:216
 aligned with Q5TLG6_9CNID | Q5TLG6 from UniProtKB/TrEMBL  Length:224

    Alignment length:218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        
         Q5TLG6_9CNID     1 MSVIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTTVFCYGNRVFAKYPENIVDYFKQSFPEGYSWERSMNYEDGGICNATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWEPSTEKLYVRDGVLKGDVNMALSLEGGGHYRCDFKTTYKAKKVVQLPDYHFVDHHIEIKSHDKDYSNVNLHEHAEAHSE 218
               SCOP domains d2poxc_ C: automated matches                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee.......hhhhhh...--hhhhh.......hhhhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pox C   1 MSVIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTTVFc--NRVFAKYPENIVDYFKQSFPEGYSWERSMNYEDGGICNATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWEPSTEKLYVRDGVLKGDVNMALSLEGGGHYRCDFKTTYKAKKVVQLPDYHFVDHHIEIKSHDKDYSNVNLHEHAEAHSE 218
                                    10        20        30        40        50        60 |  |   70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        
                                                                                        62-GYC

Chain D from PDB  Type:PROTEIN  Length:215
 aligned with Q5TLG6_9CNID | Q5TLG6 from UniProtKB/TrEMBL  Length:224

    Alignment length:217
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       
         Q5TLG6_9CNID     2 SVIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTTVFCYGNRVFAKYPENIVDYFKQSFPEGYSWERSMNYEDGGICNATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWEPSTEKLYVRDGVLKGDVNMALSLEGGGHYRCDFKTTYKAKKVVQLPDYHFVDHHIEIKSHDKDYSNVNLHEHAEAHSE 218
               SCOP domains d2poxd_ D: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) GFP-2poxD01 D:2-218                                                                                                                                                                                                       Pfam domains (1)
           Pfam domains (2) GFP-2poxD02 D:2-218                                                                                                                                                                                                       Pfam domains (2)
           Pfam domains (3) GFP-2poxD03 D:2-218                                                                                                                                                                                                       Pfam domains (3)
           Pfam domains (4) GFP-2poxD04 D:2-218                                                                                                                                                                                                       Pfam domains (4)
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee.......hhhhhh...--hhhhh.......hhhhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pox D   2 SVIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTTVFc--NRVFAKYPENIVDYFKQSFPEGYSWERSMNYEDGGICNATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWEPSTEKLYVRDGVLKGDVNMALSLEGGGHYRCDFKTTYKAKKVVQLPDYHFVDHHIEIKSHDKDYSNVNLHEHAEAHSE 218
                                    11        21        31        41        51        61|  |    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       
                                                                                       62-GYC

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: GFP-like (339)

Superfamily: GFP-like (339)

Family: automated matches (66)

Protein domain: automated matches (66)

Echinophyllia sp. [TaxId: 301887] (12)

1a	d2poxa_	A:
1b	d2poxb_	B:
1c	d2poxc_	C:
1d	d2poxd_	D:

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GFP (101)

Family: GFP (101)

Echinophyllia sp. SC22 (5)

1a	GFP-2poxD01	D:2-218
1b	GFP-2poxD02	D:2-218
1c	GFP-2poxD03	D:2-218
1d	GFP-2poxD04	D:2-218

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (Q5TLG6_9CNID | Q5TLG6)

biological process
	GO:0008218		bioluminescence		The production of light by certain enzyme-catalyzed reactions in cells.
	GO:0006091		generation of precursor metabolites and energy		The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
		GYC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
(no "Sites" information available for 2pox)

	Cis Peptide Bonds
		Gly A:48 - Pro A:49	[ RasMol ]
		Gly B:165 - Gly B:166	[ RasMol ]
		Gly B:48 - Pro B:49	[ RasMol ]
		Gly C:48 - Pro C:49	[ RasMol ]
		Gly D:48 - Pro D:49	[ RasMol ]
		Phe A:83 - Pro A:84	[ RasMol ]
		Phe B:83 - Pro B:84	[ RasMol ]
		Phe C:83 - Pro C:84	[ RasMol ]
		Phe D:83 - Pro D:84	[ RasMol ]

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	2pox
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2ie2	DRONPA, ON STATE
2iov	DRONPA, ON STATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (9, 9)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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