2Z6Y - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A PHOTOSWITCHABLE GFP-LIKE PROTEIN DRONPA IN THE BRIGHT-STATE

Authors :   A. Kikuchi, J. Jeyakanthan, J. Taka, Y. Shiro, H. Mizuno, A. Miyawaki

Date :   09 Aug 07 (Deposition) - 22 Jul 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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 :   Gfp-Like Protein, Photochromism, Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Mizuno, T. K. Mal, M. Walchli, A. Kikuchi, T. Fukano, R. Ando, J. Jeyakanthan, J. Taka, Y. Shiro, M. Ikura, A. Miyawaki
Light-Dependent Regulation Of Structural Flexibility In A Photochromic Fluorescent Protein.
Proc. Natl. Acad. Sci. Usa V. 105 9227 2008
PubMed-ID: 18574155 | Reference-DOI: 10.1073/PNAS.0709599105
(for further references see the PDB file header)

Molecule 1 - FLUORESCENT PROTEIN DRONPA
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	JM109(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DRONPA
	Organism Scientific	:	ECHINOPHYLLIA SP. SC22
	Organism Taxid	:	301887
	Synonym	:	GFP-LIKE PROTEIN 22G, PHOTOCHROMIC PROTEIN DRONPA

		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 (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

Biological Unit 1 (1, 1)

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

Biological Unit 2 (1, 1)

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

Biological Unit 3 (1, 1)

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

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	GYC	1	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 2Z6Y)

(no "SS Bond" information available for 2Z6Y)

Asymmetric 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 C:48	-	Pro C:49
6	Phe C:83	-	Pro C:84
7	Gly D:48	-	Pro D:49
8	Phe D:83	-	Pro D:84

(no "SAP(SNP)/Variant" information available for 2Z6Y)

(no "PROSITE Motif" information available for 2Z6Y)

(no "Exon" information available for 2Z6Y)

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: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 d2z6ya_ A: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......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
                 2z6y A   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       
                                                                                      61| 65                                                                                                                                                         
                                                                                       63-GYC

Chain B 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 d2z6yb_ B: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee.......hhhhhh...--............hhhhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z6y B   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       
                                                                                      61| 65                                                                                                                                                         
                                                                                       63-GYC

Chain C from PDB  Type:PROTEIN  Length:214
 aligned with Q5TLG6_9CNID | Q5TLG6 from UniProtKB/TrEMBL  Length:224

    Alignment length:216
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212      
         Q5TLG6_9CNID     3 VIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTTVFCYGNRVFAKYPENIVDYFKQSFPEGYSWERSMNYEDGGICNATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWEPSTEKLYVRDGVLKGDVNMALSLEGGGHYRCDFKTTYKAKKVVQLPDYHFVDHHIEIKSHDKDYSNVNLHEHAEAHSE 218
               SCOP domains d2z6yc_ C: automated matches                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....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
                 2z6y C   3 VIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTTVFc--NRVFAKYPENIVDYFKQSFPEGYSWERSMNYEDGGICNATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWEPSTEKLYVRDGVLKGDVNMALSLEGGGHYRCDFKTTYKAKKVVQLPDYHFVDHHIEIKSHDKDYSNVNLHEHAEAHSE 218
                                    12        22        32        42        52        63  |     72        82        92       102       112       122       132       142       152       162       172       182       192       202       212      
                                                                                     61| 65                                                                                                                                                         
                                                                                      63-GYC

Chain D from PDB  Type:PROTEIN  Length:214
 aligned with Q5TLG6_9CNID | Q5TLG6 from UniProtKB/TrEMBL  Length:224

    Alignment length:216
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212      
         Q5TLG6_9CNID     3 VIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTTVFCYGNRVFAKYPENIVDYFKQSFPEGYSWERSMNYEDGGICNATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWEPSTEKLYVRDGVLKGDVNMALSLEGGGHYRCDFKTTYKAKKVVQLPDYHFVDHHIEIKSHDKDYSNVNLHEHAEAHSE 218
               SCOP domains d2z6yd_ D: automated matches                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) GFP-2z6yD01 D:3-218                                                                                                                                                                                                      Pfam domains (1)
           Pfam domains (2) GFP-2z6yD02 D:3-218                                                                                                                                                                                                      Pfam domains (2)
           Pfam domains (3) GFP-2z6yD03 D:3-218                                                                                                                                                                                                      Pfam domains (3)
           Pfam domains (4) GFP-2z6yD04 D:3-218                                                                                                                                                                                                      Pfam domains (4)
         Sec.struct. author .....eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee.......hhhhhh...--............hhhhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2z6y D   3 VIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTTVFc--NRVFAKYPENIVDYFKQSFPEGYSWERSMNYEDGGICNATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWEPSTEKLYVRDGVLKGDVNMALSLEGGGHYRCDFKTTYKAKKVVQLPDYHFVDHHIEIKSHDKDYSNVNLHEHAEAHSE 218
                                    12        22        32        42        52        63  |     72        82        92       102       112       122       132       142       152       162       172       182       192       202       212      
                                                                                     61| 65                                                                                                                                                         
                                                                                      63-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 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	d2z6ya_	A:
1b	d2z6yb_	B:
1c	d2z6yc_	C:
1d	d2z6yd_	D:

(no "CATH Domain" information available for 2Z6Y)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GFP (101)

Family: GFP (101)

Echinophyllia sp. SC22 (5)

1a	GFP-2z6yD01	D:3-218
1b	GFP-2z6yD02	D:3-218
1c	GFP-2z6yD03	D:3-218
1d	GFP-2z6yD04	D:3-218

Asymmetric 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 Unit
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	Sites
(no "Sites" information available for 2z6y)

	Cis Peptide Bonds
		Gly A:48 - Pro A:49	[ 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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	2z6y
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Description

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Ligands, Modified Residues, Ions (1, 4)

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SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

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