4ZIN - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   GENETICALLY ENCODED PHENYL AZIDE PHOTOCHEMISTRY DRIVE POSITIVE AND NEGATIVE FUNCTIONAL MODULATION OF A RED FLUORESCENT PROTEIN

Authors :   S. C. Reddington, S. Driezis, A. M. Hartley, P. D. Watson, P. J. Rizkalla D. D. Jones

Date :   28 Apr 15 (Deposition) - 16 Sep 15 (Release) - 16 Sep 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.67

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

Keywords :   Mcherry, Photoactivation, Photodeactivation, Coloration, Fluorescence, Microscopy, Phenyl Azide, Non-Canonical Amino Acids, Optogenetics, Synchrotron, Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. C. Reddington, S. Driezis, A. M. Hartley, P. D. Watson, P. J. Rizkallah, D. D. Jones
Genetically Encoded Phenyl Azide Photochemistry Drive Positive And Negative Functional Modulation Of A Red Fluorescent Protein
Rsc Adv 2015
PubMed: search

Molecule 1 - MCHERRY FLUORESCENT PROTEIN
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	MCHERRY
	Organism Scientific	:	ANAPLASMA MARGINALE
	Organism Taxid	:	770

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 13)

No.	Name	Count	Type	Full Name
1	4OO	3	Mod. Amino Acid	4-TRIAZA-1,2-DIEN-2-IUM-1-YL-L-PHENYLALANINE
2	CH6	3	Mod. Amino Acid	{(4Z)-2-[(1S)-1-AMINO-3-(METHYLSULFANYL)PROPYL]-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
3	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
4	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	4OO	1	Mod. Amino Acid	4-TRIAZA-1,2-DIEN-2-IUM-1-YL-L-PHENYLALANINE
2	CH6	1	Mod. Amino Acid	{(4Z)-2-[(1S)-1-AMINO-3-(METHYLSULFANYL)PROPYL]-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
3	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
4	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	4OO	1	Mod. Amino Acid	4-TRIAZA-1,2-DIEN-2-IUM-1-YL-L-PHENYLALANINE
2	CH6	1	Mod. Amino Acid	{(4Z)-2-[(1S)-1-AMINO-3-(METHYLSULFANYL)PROPYL]-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
3	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
4	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 3 (4, 5)

No.	Name	Count	Type	Full Name
1	4OO	1	Mod. Amino Acid	4-TRIAZA-1,2-DIEN-2-IUM-1-YL-L-PHENYLALANINE
2	CH6	1	Mod. Amino Acid	{(4Z)-2-[(1S)-1-AMINO-3-(METHYLSULFANYL)PROPYL]-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
3	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
4	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR A:106 , THR A:108 , LYS A:123 , LEU A:124 , ARG A:125	binding site for residue SO4 A 301
02	AC2	SOFTWARE	ASP A:78 , ILE A:79 , PRO A:80 , PRO A:190 , GLY A:191 , ALA A:192 , TYR A:193 , HOH A:430 , HOH A:540	binding site for residue SO4 A 302
03	AC3	SOFTWARE	THR B:106 , THR B:108 , LYS B:123 , LEU B:124 , ARG B:125	binding site for residue SO4 B 301
04	AC4	SOFTWARE	ASN B:196 , LYS B:198 , ARG B:216 , ALA B:217 , GLU B:218	binding site for residue SO4 B 302
05	AC5	SOFTWARE	ILE C:79 , PRO C:190 , GLY C:191 , ALA C:192 , HOH C:438 , HOH C:459	binding site for residue SO4 C 301
06	AC6	SOFTWARE	THR C:106 , THR C:108 , LYS C:123	binding site for residue SO4 C 302
07	AC7	SOFTWARE	GLU B:153 , ASP B:154 , ASN C:23 , GLY C:24 , THR C:127 , ASN C:128 , HOH C:409	binding site for residue EDO C 303
08	AC8	SOFTWARE	MET B:18 , LEU B:61 , SER B:62 , PRO B:63 , GLN B:64 , SER B:69 , LYS B:70 , ARG B:95 , GLN B:109 , 4OO B:143 , GLU B:144 , ILE B:161 , GLN B:163 , ILE B:197 , LEU B:199 , GLN B:213 , GLU B:215 , HOH B:405 , HOH B:425 , HOH B:461	binding site for Di-peptide PHE B 65 and CH6 B 66
09	AC9	SOFTWARE	GLN B:42 , SER B:62 , PRO B:63 , GLN B:64 , PHE B:65 , LYS B:70 , ALA B:71 , TYR B:72 , ARG B:95 , GLN B:109 , 4OO B:143 , GLU B:144 , ILE B:161 , GLN B:163 , ILE B:197 , LEU B:199 , GLN B:213 , GLU B:215 , HOH B:405 , HOH B:425 , HOH B:461	binding site for Di-peptide CH6 B 66 and SER B 69
10	AD1	SOFTWARE	ASP B:59 , SER B:62 , PRO B:63 , CH6 B:66 , MET B:97 , MET B:141 , GLU B:144 , GLN B:163 , ARG B:164 , LEU B:165 , LYS B:166 , LEU B:199 , HOH B:430 , HOH B:443	binding site for Di-peptide GLY B 142 and 4OO B 143
11	AD2	SOFTWARE	ASP B:59 , SER B:62 , PRO B:63 , CH6 B:66 , MET B:97 , GLY B:142 , ALA B:145 , SER B:146 , GLN B:163 , ARG B:164 , LEU B:165 , LYS B:166 , HIS B:172 , LEU B:199 , HOH B:421 , HOH B:430 , HOH B:443	binding site for Di-peptide 4OO B 143 and GLU B 144
12	AD3	SOFTWARE	MET C:18 , ALA C:44 , LEU C:61 , SER C:62 , PRO C:63 , GLN C:64 , SER C:69 , LYS C:70 , TRP C:93 , ARG C:95 , SER C:146 , GLN C:163 , ILE C:197 , LEU C:199 , GLN C:213 , GLU C:215 , HOH C:401 , HOH C:421 , HOH C:433	binding site for Di-peptide PHE C 65 and CH6 C 66
13	AD4	SOFTWARE	GLN C:42 , ALA C:44 , SER C:62 , PRO C:63 , GLN C:64 , PHE C:65 , LYS C:70 , ALA C:71 , TYR C:72 , TRP C:93 , ARG C:95 , TYR C:120 , SER C:146 , GLN C:163 , ILE C:197 , LEU C:199 , GLN C:213 , GLU C:215 , HOH C:401 , HOH C:421 , HOH C:433	binding site for Di-peptide CH6 C 66 and SER C 69
14	AD5	SOFTWARE	ASP C:59 , SER C:62 , PRO C:63 , MET C:97 , PHE C:99 , MET C:141 , GLU C:144 , ARG C:164 , LEU C:165 , LYS C:166 , HOH C:437	binding site for Di-peptide GLY C 142 and 4OO C 143
15	AD6	SOFTWARE	ASP C:59 , SER C:62 , PRO C:63 , MET C:97 , PHE C:99 , GLY C:142 , ALA C:145 , SER C:146 , ARG C:164 , LEU C:165 , LYS C:166 , HOH C:401 , HOH C:423 , HOH C:437 , HOH C:483	binding site for Di-peptide 4OO C 143 and GLU C 144

(no "SS Bond" information available for 4ZIN)

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

(no "SAP(SNP)/Variant" information available for 4ZIN)

(no "PROSITE Motif" information available for 4ZIN)

(no "Exon" information available for 4ZIN)

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:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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.....eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zin A   6 AIIKEFMRFKVHMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFAWDILSPQFxSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGxEASSERMYPEDGALKGEIKQRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYNVNIKLDITSHNEDYTIVEQYERAEGRHSTG 224
                                    15        25        35        45        55        65||      77        87        97       107       117       127       137     | 147       157       167       177       187       197       207       217       
                                                                                       66-CH6                                                                    143-4OO                                                                             
                                                                                        69

Chain B from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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.....eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zin B   6 AIIKEFMRFKVHMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFAWDILSPQFxSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGxEASSERMYPEDGALKGEIKQRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYNVNIKLDITSHNEDYTIVEQYERAEGRHSTG 224
                                    15        25        35        45        55        65||      77        87        97       107       117       127       137     | 147       157       167       177       187       197       207       217       
                                                                                       66-CH6                                                                    143-4OO                                                                             
                                                                                        69

Chain C from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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.....eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zin C   6 AIIKEFMRFKVHMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFAWDILSPQFxSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGxEASSERMYPEDGALKGEIKQRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYNVNIKLDITSHNEDYTIVEQYERAEGRHSTG 224
                                    15        25        35        45        55        65||      77        87        97       107       117       127       137     | 147       157       167       177       187       197       207       217       
                                                                                       66-CH6                                                                    143-4OO                                                                             
                                                                                        69

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	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 '\|'

(no "SCOP Domain" information available for 4ZIN)

(no "CATH Domain" information available for 4ZIN)

(no "Pfam Domain" information available for 4ZIN)

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

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(no "Related Entries Specified in the PDB File" available for 4ZIN)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 13)

Sites (15, 15)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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