3NEZ - 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 :   MROJOA

Authors :   S. L. Mayo, R. A. Chica, M. M. Moore

Date :   09 Jun 10 (Deposition) - 13 Oct 10 (Release) - 04 Mar 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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 :   Rfps, Mcherry, Pi-Stacking, Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. A. Chica, M. M. Moore, B. D. Allen, S. L. Mayo
Generation Of Longer Emission Wavelength Red Fluorescent Proteins Using Computationally Designed Libraries.
Proc. Natl. Acad. Sci. Usa V. 107 20257 2010
PubMed-ID: 21059931 | Reference-DOI: 10.1073/PNAS.1013910107
(for further references see the PDB file header)

Molecule 1 - MROJOA
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-11A
	Expression System Strain	:	BL-21 GOLD (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	DISCOSOMA SP.
	Organism Taxid	:	86600

		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 (2, 8)

No.	Name	Count	Type	Full Name
1	CH6	4	Mod. Residue	{(4Z)-2-[(1S)-1-AMINO-3-(METHYLSULFANYL)PROPYL]-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
2	NRQ	4	Mod. Amino Acid	{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CH6	1	Mod. Residue	{(4Z)-2-[(1S)-1-AMINO-3-(METHYLSULFANYL)PROPYL]-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
2	NRQ	1	Mod. Amino Acid	{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	CH6	1	Mod. Residue	{(4Z)-2-[(1S)-1-AMINO-3-(METHYLSULFANYL)PROPYL]-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
2	NRQ	1	Mod. Amino Acid	{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	CH6	1	Mod. Residue	{(4Z)-2-[(1S)-1-AMINO-3-(METHYLSULFANYL)PROPYL]-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
2	NRQ	1	Mod. Amino Acid	{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID

Biological Unit 4 (2, 2)

No.	Name	Count	Type	Full Name
1	CH6	1	Mod. Residue	{(4Z)-2-[(1S)-1-AMINO-3-(METHYLSULFANYL)PROPYL]-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
2	NRQ	1	Mod. Amino Acid	{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID

(no "Site" information available for 3NEZ)

(no "SS Bond" information available for 3NEZ)

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 3NEZ)

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

(no "Exon" information available for 3NEZ)

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:216
 aligned with D1MPT3_DISSP | D1MPT3 from UniProtKB/TrEMBL  Length:236

    Alignment length:218
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219        
         D1MPT3_DISSP    10 MAIIKEFMRFKVHMEGSVNGHVFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFTWDILSPQFMYGSNAYVKHPADIPDYFKLSFPEGFKWERVMKFEDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEALSERMYPEDGALKGEVKPRVKLKDGGHYDAEVKTTYKAKKPVQLPGAYNVNRKLDITSHNEDYTIVEQYERAEGRHS 227
               SCOP domains d3neza_ A: automated matches                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh-.-............hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nez A   5 MAIIKEFMRFKTHMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFAWDILSPQF-m-SKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGEFIYKVKLHGTNFPSDGPVMQKKTMGWEASSERMYPEDGALKGEIKLRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYNANYKLDITSHNEDYTIVEQYERCEGRHS 222
                                    14        24        34        44        54        64| | |   74        84        94       104       114       124       134       144       154       164       174       184       194       204       214        
                                                                                       65 | |                                                                                                                                                         
                                                                                         67-NRQ                                                                                                                                                       
                                                                                           69

Chain B from PDB  Type:PROTEIN  Length:215
 aligned with D1MPT3_DISSP | D1MPT3 from UniProtKB/TrEMBL  Length:236

    Alignment length:217
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       
         D1MPT3_DISSP    11 AIIKEFMRFKVHMEGSVNGHVFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFTWDILSPQFMYGSNAYVKHPADIPDYFKLSFPEGFKWERVMKFEDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEALSERMYPEDGALKGEVKPRVKLKDGGHYDAEVKTTYKAKKPVQLPGAYNVNRKLDITSHNEDYTIVEQYERAEGRHS 227
               SCOP domains d3nezb_ B: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh-.-hhhhh.......hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee..................eeeeeeee..eeeeeeeeeee.hhh.eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nez B   6 AIIKEFMRFKTHMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFAWDILSPQF-m-SKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGEFIYKVKLHGTNFPSDGPVMQKKTMGWEASSERMYPEDGALKGEIKLRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYNANYKLDITSHNEDYTIVEQYERCEGRHS 222
                                    15        25        35        45        55        65 | |    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       
                                                                                      65 | |                                                                                                                                                         
                                                                                        67-NRQ                                                                                                                                                       
                                                                                          69

Chain C from PDB  Type:PROTEIN  Length:215
 aligned with D1MPT3_DISSP | D1MPT3 from UniProtKB/TrEMBL  Length:236

    Alignment length:217
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       
         D1MPT3_DISSP    11 AIIKEFMRFKVHMEGSVNGHVFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFTWDILSPQFMYGSNAYVKHPADIPDYFKLSFPEGFKWERVMKFEDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEALSERMYPEDGALKGEVKPRVKLKDGGHYDAEVKTTYKAKKPVQLPGAYNVNRKLDITSHNEDYTIVEQYERAEGRHS 227
               SCOP domains d3nezc_ C: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh-.-hhhhh.......hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nez C   6 AIIKEFMRFKTHMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFAWDILSPQF-m-SKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGEFIYKVKLHGTNFPSDGPVMQKKTMGWEASSERMYPEDGALKGEIKLRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYNANYKLDITSHNEDYTIVEQYERCEGRHS 222
                                    15        25        35        45        55        65 | |    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       
                                                                                      65 | |                                                                                                                                                         
                                                                                        67-NRQ                                                                                                                                                       
                                                                                          69

Chain D from PDB  Type:PROTEIN  Length:216
 aligned with D1MPT3_DISSP | D1MPT3 from UniProtKB/TrEMBL  Length:236

    Alignment length:218
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219        
         D1MPT3_DISSP    10 MAIIKEFMRFKVHMEGSVNGHVFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFTWDILSPQFMYGSNAYVKHPADIPDYFKLSFPEGFKWERVMKFEDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEALSERMYPEDGALKGEVKPRVKLKDGGHYDAEVKTTYKAKKPVQLPGAYNVNRKLDITSHNEDYTIVEQYERAEGRHS 227
               SCOP domains d3nezd_ D: automated matches                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeeeeeee.....eeeeeeeeee......hhhhhhhhh-.-............hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nez D   5 MAIIKEFMRFKTHMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFAWDILSPQF-m-SKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGEFIYKVKLHGTNFPSDGPVMQKKTMGWEASSERMYPEDGALKGEIKLRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYNANYKLDITSHNEDYTIVEQYERCEGRHS 222
                                    14        24        34        44        54        64| | |   74        84        94       104       114       124       134       144       154       164       174       184       194       204       214        
                                                                                       65 | |                                                                                                                                                         
                                                                                         67-NRQ                                                                                                                                                       
                                                                                           69

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: automated matches (102)

Coral (Discosoma sp.) [TaxId: 86600] (17)

1a	d3neza_	A:
1b	d3nezb_	B:
1c	d3nezc_	C:
1d	d3nezd_	D:

(no "CATH Domain" information available for 3NEZ)

(no "Pfam Domain" information available for 3NEZ)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (D1MPT3_DISSP | D1MPT3)

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 3nez)

	Cis Peptide Bonds
		Gly A:52 - Pro A:53	[ RasMol ]
		Gly B:52 - Pro B:53	[ RasMol ]
		Gly C:52 - Pro C:53	[ RasMol ]
		Gly D:52 - Pro D:53	[ 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 ]

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		Biological Unit 4	[ Jena3D ]

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	3nez
		Family and Domain Information	:	ProDom \| SYSTERS
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	D1MPT3_DISSP \| D1MPT3
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	D1MPT3_DISSP \| D1MPT3	:	3kcs 3kct 3lf3 3lf4 3ned 5h87 5h89

3neb	MROUGE
3nf0	MPLUM

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

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