3K1K - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   GREEN FLUORESCENT PROTEIN BOUND TO ENHANCER NANOBODY

Authors :   A. Kirchhofer, J. Helma, K. Schmidthals, C. Frauer, S. Cui, A. Karcher, S. Muyldermans, C. C. Delucci, M. C. Cardoso, H. Leonhardt, K. -P. Hopf U. Rothbauer

Date :   28 Sep 09 (Deposition) - 08 Dec 09 (Release) - 25 Jan 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

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

Keywords :   Nanobody, Antibody-Complex, Chromophore, Luminescence, Photoprotein, Luminescent Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Kirchhofer, J. Helma, K. Schmidthals, C. Frauer, S. Cui, A. Karcher M. Pellis, S. Muyldermans, C. C. Deulcci, M. C. Cardoso, H. Leonhardt, K. -P. Hopfner, U. Rothbauer
Modulation Of Protein Properties In Living Cells Using Nanobodies
Nat. Struct. Mol. Biol. V. 17 133 2010
PubMed-ID: 20010839 | Reference-DOI: 10.1038/NSMB.1727

Molecule 1 - GREEN FLUORESCENT PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRSET5D
	Expression System Strain	:	B834 (ROSETTA (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GFP
	Mutation	:	YES
	Organism Scientific	:	AEQUOREA VICTORIA
	Organism Taxid	:	6100

Molecule 2 - ENHANCER
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PHEN6
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	CAMELUS DROMEDARIUS
	Organism Taxid	:	9838

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	GYS	2	Mod. Amino Acid	[(4Z)-2-(1-AMINO-2-HYDROXYETHYL)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	GYS	1	Mod. Amino Acid	[(4Z)-2-(1-AMINO-2-HYDROXYETHYL)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
2	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	GYS	1	Mod. Amino Acid	[(4Z)-2-(1-AMINO-2-HYDROXYETHYL)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
2	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 3K1K)

Asymmetric Unit

No.	Residues
1	C:22	-	C:92
2	D:22	-	D:92

Asymmetric Unit

No.	Residues
1	Mse A:88	-	Pro A:89
2	Mse B:88	-	Pro B:89

Asymmetric Unit (4, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_GFP_AEQVI_001 *	F	100	Y	GFP_AEQVI	---	---	A/B	F	100	Y
2	UniProt	VAR_GFP_AEQVI_002 *	T	108	S	GFP_AEQVI	---	---	A/B	T	108	S
3	UniProt	VAR_GFP_AEQVI_003 *	L	141	M	GFP_AEQVI	---	---	A/B	L	141	M
4	UniProt	VAR_GFP_AEQVI_004 *	V	219	I	GFP_AEQVI	---	---	A/B	V	219	I
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_GFP_AEQVI_001 *	F	100	Y	GFP_AEQVI	---	---	A	F	100	Y
2	UniProt	VAR_GFP_AEQVI_002 *	T	108	S	GFP_AEQVI	---	---	A	T	108	S
3	UniProt	VAR_GFP_AEQVI_003 *	L	141	M	GFP_AEQVI	---	---	A	L	141	M
4	UniProt	VAR_GFP_AEQVI_004 *	V	219	I	GFP_AEQVI	---	---	A	V	219	I
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_GFP_AEQVI_001 *	F	100	Y	GFP_AEQVI	---	---	B	F	100	Y
2	UniProt	VAR_GFP_AEQVI_002 *	T	108	S	GFP_AEQVI	---	---	B	T	108	S
3	UniProt	VAR_GFP_AEQVI_003 *	L	141	M	GFP_AEQVI	---	---	B	L	141	M
4	UniProt	VAR_GFP_AEQVI_004 *	V	219	I	GFP_AEQVI	---	---	B	V	219	I
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 3K1K)

(no "Exon" information available for 3K1K)

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:225
 aligned with GFP_AEQVI | P42212 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:227
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       
            GFP_AEQVI     3 KGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGI 229
               SCOP domains d3k1ka_ A: Green fluorescent protein, GFP                                                                                                                                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh.eeeeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh...-.-hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee...................eeeeeeeehhhheeeeeeeeeee.....eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------Y-------S--------------------------------M-----------------------------------------------------------------------------I---------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k1k A   3 KGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTF-s-VQCFSRYPDHmKRHDFFKSAmPEGYVQERTISFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIKANFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHmVLLEFVTAAGI 229
                                    12        22        32        42        52        62 | | |  72     |  82     |  92       102       112       122       132       142       152       162       172       182       192       202       212     | 222       
                                                                                        64 | |        78-MSE    88-MSE                                                                                                                           218-MSE       
                                                                                          66-GYS                                                                                                                                                               
                                                                                            68

Chain B from PDB  Type:PROTEIN  Length:225
 aligned with GFP_AEQVI | P42212 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:227
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       
            GFP_AEQVI     3 KGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGI 229
               SCOP domains d3k1kb_ B: Green fluorescent protein, GFP                                                                                                                                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --GFP-3k1kB01 B:5-229                                                                                                                                                                                                               Pfam domains (1)
           Pfam domains (2) --GFP-3k1kB02 B:5-229                                                                                                                                                                                                               Pfam domains (2)
         Sec.struct. author .hhhhhh.eeeeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh...-.-hhhhh..hhhhhhhh.hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee...................eeeeeeeehhhheeeeeeeeeee.....eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------Y-------S--------------------------------M-----------------------------------------------------------------------------I---------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k1k B   3 KGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTF-s-VQCFSRYPDHmKRHDFFKSAmPEGYVQERTISFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIKANFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHmVLLEFVTAAGI 229
                                    12        22        32        42        52        62 | | |  72     |  82     |  92       102       112       122       132       142       152       162       172       182       192       202       212     | 222       
                                                                                        64 | |        78-MSE    88-MSE                                                                                                                           218-MSE       
                                                                                          66-GYS                                                                                                                                                               
                                                                                            68

Chain C from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains d3k1kc_ C: automated matches                                                                                       SCOP domains
               CATH domains 3k1kC00 C:1-112 Immunoglobulins                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeee......eeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee...eee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 3k1k C   1 QVQLVESGGALVQPGGSLRLSCAASGFPVNRYSMRWYRQAPGKEREWVAGMSSAGDRSSYEDSVKGRFTISRDDARNTVYLQMNSLKPEDTAVYYCNVNVGFEYWGQGTQVTVS 112
                                    10        20        30        40        50  |     59        69        79   |||  86        96 ||    108    
                                                                              52A                            82A||              98|           
                                                                                                              82B|              101           
                                                                                                               82C

Chain D from PDB  Type:PROTEIN  Length:115
                                                                                                                                                   
               SCOP domains d3k1kd_ D: automated matches                                                                                        SCOP domains
               CATH domains 3k1kD00 D:1-113 Immunoglobulins                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee...eee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 3k1k D   1 QVQLVESGGALVQPGGSLRLSCAASGFPVNRYSMRWYRQAPGKEREWVAGMSSAGDRSSYEDSVKGRFTISRDDARNTVYLQMNSLKPEDTAVYYCNVNVGFEYWGQGTQVTVSS 113
                                    10        20        30        40        50  |     59        69        79   |||  86        96 ||    108     
                                                                              52A                            82A||              98|            
                                                                                                              82B|              101            
                                                                                                               82C

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Aequorea victoria. Organism_taxid: 6100. (1)

1a	3k1kC00	C:1-112
1b	3k1kD00	D:1-113

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GFP (101)

Family: GFP (101)

Aequorea victoria (Jellyfish) (53)

1a	GFP-3k1kB01	B:5-229
1b	GFP-3k1kB02	B:5-229

Asymmetric Unit(hide GO term definitions)

Chain A,B (GFP_AEQVI | P42212)

molecular function
	GO:0003674	molecular_function	Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
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.
	GO:0018298	protein-chromophore linkage	The covalent or noncovalent attachment of a chromophore to a protein.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Sites
(no "Sites" information available for 3k1k)

	Cis Peptide Bonds
		Mse A:88 - Pro A:89	[ RasMol ]
		Mse B:88 - Pro B:89	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (0, 0)

SS Bonds (2, 2)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (4, 8)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 4)

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