2RH7 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURES OF THE LUCIFERASE AND GREEN FLUORESCENT PROTEIN FROM RENILLA RENIFORMIS

Authors :   A. M. Loening, T. D. Fenn, S. S. Gambhir

Date :   06 Oct 07 (Deposition) - 23 Oct 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. M. Loening, T. D. Fenn, S. S. Gambhir
Crystal Structures Of The Luciferase And Green Fluorescent Protein From Renilla Reniformis.
J. Mol. Biol. V. 374 1017 2007
PubMed-ID: 17980388 | Reference-DOI: 10.1016/J.JMB.2007.09.078
(for further references see the PDB file header)

Molecule 1 - GREEN FLUORESCENT PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBAD
	Expression System Strain	:	LMG194
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GFP
	Organism Scientific	:	RENILLA RENIFORMIS
	Organism Taxid	:	6136

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

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

Biological Unit 1 (1, 2)

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

Biological Unit 2 (1, 2)

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

(no "Site" information available for 2RH7)

(no "SS Bond" information available for 2RH7)

Asymmetric Unit

No.	Residues
1	Ala A:52	-	Pro A:53
2	Phe A:87	-	Pro A:88
3	Ala B:52	-	Pro B:53
4	Phe B:87	-	Pro B:88
5	Ala C:52	-	Pro C:53
6	Phe C:87	-	Pro C:88
7	Ala D:52	-	Pro D:53
8	Phe D:87	-	Pro D:88
9	Gly D:116	-	Gly D:116

(no "SAP(SNP)/Variant" information available for 2RH7)

(no "PROSITE Motif" information available for 2RH7)

(no "Exon" information available for 2RH7)

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:212
 aligned with Q963I9_RENRE | Q963I9 from UniProtKB/TrEMBL  Length:233

    Alignment length:220
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226
         Q963I9_RENRE     7 GLKEVMPTKINLEGLVGDHAFSMEGVGEGNILEGTQEVKISVTKGAPLPFAFDIVSVAFSYGNRAYTGYPEEISDYFLQSFPEGFTYERNIRYQDGGTAIVKSDISLEDGKFIVNVDFKAKDLRRMGPVMQQDIVGMQPSYESMYTNVTSVIGECIIAFKLQTGKHFTYHMRTVYKSKKPVETMPLYHFIQHRLVKTNVDTASGYVVQHETAIAAHSTIK 226
               SCOP domains d2rh7a1 A:7-226 Green fluorescent protein, GFP                                                                                                                                                                               SCOP domains
               CATH domains 2rh7A00 A:7-226 Green Fluorescent Protein                                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhh....--..............hhhhh...eeeeeeeee....eeeeeeeeee.-..eeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeee.-----..eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rh7 A   7 GLKEVMPTKINLEGLVGDHAFSMEGVGEGNILEGTQEVKISVTKGAPLPFAFDIVSVAFg--NRAYTGYPEEISDYFLQSFPEGFTYERNIRYQDGGTAIVKSDISLE-GKFIVNVDFKAKDLRRMGPVMQQDIVGMQPSYESMYTNVTSVIGECIIAFKLQTGKHFTYHMRTVYKSKKPVETMPLYHFIQHRLVKTNV-----YVVQHETAIAAHSTIK 226
                                    16        26        36        46        56        66  |     76        86        96       106       116       126       136       146       156       166       176       186       196        |-    |  216       226
                                                                                      66-CRO                                         114 |                                                                                      205   211               
                                                                                                                                       116

Chain B from PDB  Type:PROTEIN  Length:213
 aligned with Q963I9_RENRE | Q963I9 from UniProtKB/TrEMBL  Length:233

    Alignment length:220
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226
         Q963I9_RENRE     7 GLKEVMPTKINLEGLVGDHAFSMEGVGEGNILEGTQEVKISVTKGAPLPFAFDIVSVAFSYGNRAYTGYPEEISDYFLQSFPEGFTYERNIRYQDGGTAIVKSDISLEDGKFIVNVDFKAKDLRRMGPVMQQDIVGMQPSYESMYTNVTSVIGECIIAFKLQTGKHFTYHMRTVYKSKKPVETMPLYHFIQHRLVKTNVDTASGYVVQHETAIAAHSTIK 226
               SCOP domains d2rh7b_ B: Green fluorescent protein, GFP                                                                                                                                                                                    SCOP domains
               CATH domains 2rh7B00 B:7-226 Green Fluorescent Protein                                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhh....--..............hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee.....hhhhhh.eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeee.-----.eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rh7 B   7 GLKEVMPTKINLEGLVGDHAFSMEGVGEGNILEGTQEVKISVTKGAPLPFAFDIVSVAFg--NRAYTGYPEEISDYFLQSFPEGFTYERNIRYQDGGTAIVKSDISLEDGKFIVNVDFKAKDLRRMGPVMQQDIVGMQPSYESMYTNVTSVIGECIIAFKLQTGKHFTYHMRTVYKSKKPVETMPLYHFIQHRLVKTNV-----YVVQHETAIAAHSTIK 226
                                    16        26        36        46        56        66  |     76        86        96       106       116       126       136       146       156       166       176       186       196        |-    |  216       226
                                                                                      66-CRO                                                                                                                                    205   211

Chain C from PDB  Type:PROTEIN  Length:212
 aligned with Q963I9_RENRE | Q963I9 from UniProtKB/TrEMBL  Length:233

    Alignment length:220
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226
         Q963I9_RENRE     7 GLKEVMPTKINLEGLVGDHAFSMEGVGEGNILEGTQEVKISVTKGAPLPFAFDIVSVAFSYGNRAYTGYPEEISDYFLQSFPEGFTYERNIRYQDGGTAIVKSDISLEDGKFIVNVDFKAKDLRRMGPVMQQDIVGMQPSYESMYTNVTSVIGECIIAFKLQTGKHFTYHMRTVYKSKKPVETMPLYHFIQHRLVKTNVDTASGYVVQHETAIAAHSTIK 226
               SCOP domains d2rh7c_ C: Green fluorescent protein, GFP                                                                                                                                                                                    SCOP domains
               CATH domains 2rh7C00 C:7-226 Green Fluorescent Protein                                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhh....--..............hhhhh...eeeeeeeee....eeeeeeeeee.-..eeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeee.-----..eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rh7 C   7 GLKEVMPTKINLEGLVGDHAFSMEGVGEGNILEGTQEVKISVTKGAPLPFAFDIVSVAFg--NRAYTGYPEEISDYFLQSFPEGFTYERNIRYQDGGTAIVKSDISLE-GKFIVNVDFKAKDLRRMGPVMQQDIVGMQPSYESMYTNVTSVIGECIIAFKLQTGKHFTYHMRTVYKSKKPVETMPLYHFIQHRLVKTNV-----YVVQHETAIAAHSTIK 226
                                    16        26        36        46        56        66  |     76        86        96       106       116       126       136       146       156       166       176       186       196        |-    |  216       226
                                                                                      66-CRO                                         114 |                                                                                      205   211               
                                                                                                                                       116

Chain D from PDB  Type:PROTEIN  Length:212
 aligned with Q963I9_RENRE | Q963I9 from UniProtKB/TrEMBL  Length:233

    Alignment length:220
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226
         Q963I9_RENRE     7 GLKEVMPTKINLEGLVGDHAFSMEGVGEGNILEGTQEVKISVTKGAPLPFAFDIVSVAFSYGNRAYTGYPEEISDYFLQSFPEGFTYERNIRYQDGGTAIVKSDISLEDGKFIVNVDFKAKDLRRMGPVMQQDIVGMQPSYESMYTNVTSVIGECIIAFKLQTGKHFTYHMRTVYKSKKPVETMPLYHFIQHRLVKTNVDTASGYVVQHETAIAAHSTIK 226
               SCOP domains d2rh7d_ D: Green fluorescent protein, GFP                                                                                                                                                                                    SCOP domains
               CATH domains 2rh7D00 D:7-226 Green Fluorescent Protein                                                                                                                                                                                    CATH domains
           Pfam domains (1) GFP-2rh7D01 D:7-223                                                                                                                                                                                                      --- Pfam domains (1)
           Pfam domains (2) GFP-2rh7D02 D:7-223                                                                                                                                                                                                      --- Pfam domains (2)
           Pfam domains (3) GFP-2rh7D03 D:7-223                                                                                                                                                                                                      --- Pfam domains (3)
           Pfam domains (4) GFP-2rh7D04 D:7-223                                                                                                                                                                                                      --- Pfam domains (4)
         Sec.struct. author ....eeeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhh....--............hhhhhhh...eeeeeeeee....eeeeeeeee..-..eeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeee.-----..eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rh7 D   7 GLKEVMPTKINLEGLVGDHAFSMEGVGEGNILEGTQEVKISVTKGAPLPFAFDIVSVAFg--NRAYTGYPEEISDYFLQSFPEGFTYERNIRYQDGGTAIVKSDISLE-GKFIVNVDFKAKDLRRMGPVMQQDIVGMQPSYESMYTNVTSVIGECIIAFKLQTGKHFTYHMRTVYKSKKPVETMPLYHFIQHRLVKTNV-----YVVQHETAIAAHSTIK 226
                                    16        26        36        46        56        66  |     76        86        96       106       116       126       136       146       156       166       176       186       196        |-    |  216       226
                                                                                      66-CRO                                         114 |                                                                                      205   211               
                                                                                                                                       116

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: Fluorescent proteins (271)

Protein domain: Green fluorescent protein, GFP (161)

Renilla reniformis [TaxId: 6136] (1)

1a	d2rh7a1	A:7-226
1b	d2rh7b_	B:
1c	d2rh7c_	C:
1d	d2rh7d_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Green Fluorescent Protein (102)

Homologous Superfamily: Green Fluorescent Protein (102)

Renilla reniformis. Organism_taxid: 6136. (1)

1a	2rh7B00	B:7-226
1b	2rh7A00	A:7-226
1c	2rh7C00	C:7-226
1d	2rh7D00	D:7-226

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GFP (101)

Family: GFP (101)

Renilla reniformis (Sea pansy) (1)

1a	GFP-2rh7D01	D:7-223
1b	GFP-2rh7D02	D:7-223
1c	GFP-2rh7D03	D:7-223
1d	GFP-2rh7D04	D:7-223

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q963I9_RENRE | Q963I9)

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 2rh7)

	Cis Peptide Bonds
		Ala A:52 - Pro A:53	[ RasMol ]
		Ala B:52 - Pro B:53	[ RasMol ]
		Ala C:52 - Pro C:53	[ RasMol ]
		Ala D:52 - Pro D:53	[ RasMol ]
		Gly D:116 - Gly D:116	[ RasMol ]
		Phe A:87 - Pro A:88	[ RasMol ]
		Phe B:87 - Pro B:88	[ RasMol ]
		Phe C:87 - Pro C:88	[ RasMol ]
		Phe D:87 - Pro D:88	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
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	2rh7
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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

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