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(-) Description

Title :  CRYSTAL STRUCTURE OF FLUORESCENT PROTEIN UNAG WILD TYPE
 
Authors :  A. Kumagai, R. Ando, H. Miyatake, A. Miyawaki
Date :  26 Nov 12  (Deposition) - 19 Jun 13  (Release) - 04 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Keywords :  Fluorescent Protein, Bilirubin Binding Protein, Lipocalin, Beta Barrel, Fatty Acid Binding Protein-Like, Cytosol (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kumagai, R. Ando, H. Miyatake, P. Greimel, T. Kobayashi, Y. Hirabayashi, T. Shimogori, A. Miyawaki
A Bilirubin-Inducible Fluorescent Protein From Eel Muscle
Cell(Cambridge, Mass. ) V. 153 1602 2013
PubMed-ID: 23768684  |  Reference-DOI: 10.1016/J.CELL.2013.05.038

(-) Compounds

Molecule 1 - BILIRUBIN-INDUCIBLE FLUORESCENT PROTEIN UNAG
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-2T
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: JAPANESE EEL
    Organism Scientific: ANGUILLA JAPONICA
    Organism Taxid: 7937
    Synonym: UNAGI GREEN FLUORESCENT PROTEIN, UNAG

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A     
Biological Unit 2 (1x):  B    
Biological Unit 3 (1x):   C   
Biological Unit 4 (1x):    D  
Biological Unit 5 (1x):     E 
Biological Unit 6 (1x):      F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 15)

Asymmetric Unit (2, 15)
No.NameCountTypeFull Name
1BLR6Ligand/Ion3-[5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-2-[[5-[(Z)-(3-ETHENYL-4-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-3-(3-HYDROXY-3-OXOPROPYL)-4-METHYL-1H-PYRROL-2-YL]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC ACID
2PEG9Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1BLR1Ligand/Ion3-[5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-2-[[5-[(Z)-(3-ETHENYL-4-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-3-(3-HYDROXY-3-OXOPROPYL)-4-METHYL-1H-PYRROL-2-YL]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC ACID
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1BLR1Ligand/Ion3-[5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-2-[[5-[(Z)-(3-ETHENYL-4-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-3-(3-HYDROXY-3-OXOPROPYL)-4-METHYL-1H-PYRROL-2-YL]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC ACID
2PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1BLR1Ligand/Ion3-[5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-2-[[5-[(Z)-(3-ETHENYL-4-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-3-(3-HYDROXY-3-OXOPROPYL)-4-METHYL-1H-PYRROL-2-YL]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC ACID
2PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
1BLR1Ligand/Ion3-[5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-2-[[5-[(Z)-(3-ETHENYL-4-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-3-(3-HYDROXY-3-OXOPROPYL)-4-METHYL-1H-PYRROL-2-YL]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC ACID
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 5 (2, 2)
No.NameCountTypeFull Name
1BLR1Ligand/Ion3-[5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-2-[[5-[(Z)-(3-ETHENYL-4-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-3-(3-HYDROXY-3-OXOPROPYL)-4-METHYL-1H-PYRROL-2-YL]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC ACID
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 6 (2, 4)
No.NameCountTypeFull Name
1BLR1Ligand/Ion3-[5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-2-[[5-[(Z)-(3-ETHENYL-4-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-3-(3-HYDROXY-3-OXOPROPYL)-4-METHYL-1H-PYRROL-2-YL]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC ACID
2PEG3Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:17 , LEU A:30 , THR A:37 , LEU A:41 , ILE A:43 , VAL A:53 , ILE A:55 , ASN A:57 , THR A:61 , PRO A:79 , SER A:80 , LEU A:97 , ARG A:112 , LEU A:119 , ARG A:132 , TYR A:134 , HOH A:302 , HOH A:310 , HOH A:314BINDING SITE FOR RESIDUE BLR A 201
02AC2SOFTWAREGLY A:18 , GLU A:19 , LYS A:22 , ASP A:32 , ASP A:35 , HOH A:339 , HOH A:392 , HOH A:506 , HOH A:547BINDING SITE FOR RESIDUE PEG A 202
03AC3SOFTWAREPHE B:17 , LEU B:30 , THR B:37 , LEU B:41 , ILE B:43 , VAL B:53 , ILE B:55 , ASN B:57 , THR B:61 , PRO B:79 , SER B:80 , LEU B:97 , ARG B:112 , LEU B:119 , ARG B:132 , TYR B:134 , HOH B:304 , HOH B:309 , HOH B:484BINDING SITE FOR RESIDUE BLR B 201
04AC4SOFTWAREASP B:64 , THR B:65 , PHE B:78 , HOH B:319 , HOH B:333 , HOH B:339 , HOH B:341 , HOH B:347 , HOH B:460 , HOH B:519 , ASP D:64 , THR D:65 , PHE D:78 , HOH D:342BINDING SITE FOR RESIDUE PEG B 202
05AC5SOFTWAREPRO B:59 , PHE B:62 , HOH B:458 , ASP C:13 , HIS C:15 , VAL C:131 , ARG C:132 , SER C:133 , HOH C:430 , HOH C:433 , HOH C:633 , HOH C:634BINDING SITE FOR RESIDUE PEG B 203
06AC6SOFTWAREASP B:127 , HOH B:567BINDING SITE FOR RESIDUE PEG B 204
07AC7SOFTWAREPHE C:17 , LEU C:30 , THR C:37 , LEU C:41 , VAL C:53 , ILE C:55 , ASN C:57 , THR C:61 , VAL C:67 , PRO C:79 , SER C:80 , ARG C:112 , LEU C:119 , ARG C:132 , TYR C:134 , HOH C:304 , HOH C:309 , HOH C:312BINDING SITE FOR RESIDUE BLR C 200
08AC8SOFTWAREPHE D:17 , LEU D:30 , THR D:37 , LEU D:41 , ILE D:43 , ILE D:55 , ASN D:57 , THR D:61 , PRO D:79 , SER D:80 , ARG D:112 , LEU D:119 , ARG D:132 , TYR D:134 , HOH D:311 , HOH D:429 , HOH D:504BINDING SITE FOR RESIDUE BLR D 201
09AC9SOFTWARELEU A:92 , HOH A:345 , HOH A:376 , ASN D:91 , VAL D:98 , VAL D:100 , THR D:109 , HOH D:378 , HOH D:549 , HOH D:551 , HOH D:552BINDING SITE FOR RESIDUE PEG D 202
10BC1SOFTWAREPHE E:17 , LEU E:30 , THR E:37 , LEU E:41 , ILE E:43 , VAL E:53 , ILE E:55 , ASN E:57 , THR E:61 , PRO E:79 , SER E:80 , ASP E:81 , LEU E:97 , ARG E:112 , LEU E:119 , ARG E:132 , TYR E:134 , HOH E:310 , HOH E:312 , HOH E:511BINDING SITE FOR RESIDUE BLR E 201
11BC2SOFTWAREPHE C:78 , HOH C:369 , HOH C:468 , HOH C:488 , THR E:65 , GLN E:66 , HOH E:323 , HOH E:347 , HOH E:507 , HOH E:520 , HOH E:528 , HOH E:556 , HOH E:596 , HOH E:620BINDING SITE FOR RESIDUE PEG E 202
12BC3SOFTWAREPHE F:17 , LEU F:30 , THR F:37 , LEU F:41 , ILE F:43 , VAL F:53 , ILE F:55 , ASN F:57 , THR F:61 , PRO F:79 , SER F:80 , ARG F:112 , LEU F:119 , ARG F:132 , TYR F:134 , HOH F:312 , HOH F:316 , HOH F:325BINDING SITE FOR RESIDUE BLR F 201
13BC4SOFTWAREVAL C:98 , VAL C:100 , THR C:109 , HOH C:523 , LEU F:92 , GLY F:94 , HOH F:340 , HOH F:544BINDING SITE FOR RESIDUE PEG F 202
14BC5SOFTWAREPHE A:78 , HOH A:500 , HOH A:520 , ASP F:64 , THR F:65 , HOH F:321 , HOH F:328 , HOH F:336 , HOH F:572 , HOH F:573 , HOH F:574 , HOH F:583BINDING SITE FOR RESIDUE PEG F 203
15BC6SOFTWAREHOH C:438 , HOH C:559 , LYS F:96 , VAL F:111 , GLU F:113 , THR F:122 , HOH F:323 , HOH F:380BINDING SITE FOR RESIDUE PEG F 204

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4I3B)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Pro A:59 -Pro A:60
2Pro B:59 -Pro B:60
3Pro C:59 -Pro C:60
4Pro D:59 -Pro D:60
5Pro E:59 -Pro E:60
6Pro F:59 -Pro F:60

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I3B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I3B)

(-) Exons   (0, 0)

(no "Exon" information available for 4I3B)

(-) Sequences/Alignments

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:139
                                                                                                                                                                           
               SCOP domains d4i3ba_ A: automated matches                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhheeeeeeeeehhhhhhhhh..hhhhhhhhhhh..eeeeeee...eeeeeee.......eeeeeee....eee........eeeeeeee..eeeeeeee..eeeeeeeeee..eeeeeeee..eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i3b A   1 MVEKFVGTWKIADSHNFGEYLKAIGAPKELSDGGDATTPTLYISQKDGDKMTVKIENGPPTFLDTQVKFKLGEEFDEFPSDRRKGVKSVVNLVGEKLVYVQKWDGKETTYVREIKDGKLVVTLTMGDVVAVRSYRRATE 139
                                    10        20        30        40        50        60        70        80        90       100       110       120       130         


Chain B from PDB  Type:PROTEIN  Length:138
                                                                                                                                                                          
               SCOP domains d4i3bb_ B: automated matches                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhheeeeeeeeehhhhhhhhh..hhhhhhhhhhh..eeeeeee...eeeeeee.......eeeeeee....eee........eeeeeeee..eeeeeeee..eeeeeeeeee..eeeeeeee..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4i3b B   1 MVEKFVGTWKIADSHNFGEYLKAIGAPKELSDGGDATTPTLYISQKDGDKMTVKIENGPPTFLDTQVKFKLGEEFDEFPSDRRKGVKSVVNLVGEKLVYVQKWDGKETTYVREIKDGKLVVTLTMGDVVAVRSYRRAT 138
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        


Chain C from PDB  Type:PROTEIN  Length:138
                                                                                                                                                                          
               SCOP domains d4i3bc_ C: automated matches                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhheeeeeeeeehhhhhhhhh..hhhhhhhhhhh..eeeeeee...eeeeeee.......eeeeeee....eee........eeeeeeee..eeeeeeee..eeeeeeeeee..eeeeeeee..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4i3b C   1 MVEKFVGTWKIADSHNFGEYLKAIGAPKELSDGGDATTPTLYISQKDGDKMTVKIENGPPTFLDTQVKFKLGEEFDEFPSDRRKGVKSVVNLVGEKLVYVQKWDGKETTYVREIKDGKLVVTLTMGDVVAVRSYRRAT 138
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        


Chain D from PDB  Type:PROTEIN  Length:138
                                                                                                                                                                          
               SCOP domains d4i3bd_ D: automated matches                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhheeeeeeeeehhhhhhhhh..hhhhhhhhhhh..eeeeeee...eeeeeee.......eeeeeee....eee........eeeeeeee..eeeeeeee..eeeeeeeeee..eeeeeeee..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4i3b D   1 MVEKFVGTWKIADSHNFGEYLKAIGAPKELSDGGDATTPTLYISQKDGDKMTVKIENGPPTFLDTQVKFKLGEEFDEFPSDRRKGVKSVVNLVGEKLVYVQKWDGKETTYVREIKDGKLVVTLTMGDVVAVRSYRRAT 138
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        


Chain E from PDB  Type:PROTEIN  Length:139
                                                                                                                                                                           
               SCOP domains d4i3be_ E: automated matches                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhheeeeeeeeehhhhhhhhh..hhhhhhhhhh...eeeeeee...eeeeeee.......eeeeeee....eee........eeeeeeee..eeeeeeee..eeeeeeeeee..eeeeeeee..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i3b E   1 MVEKFVGTWKIADSHNFGEYLKAIGAPKELSDGGDATTPTLYISQKDGDKMTVKIENGPPTFLDTQVKFKLGEEFDEFPSDRRKGVKSVVNLVGEKLVYVQKWDGKETTYVREIKDGKLVVTLTMGDVVAVRSYRRATE 139
                                    10        20        30        40        50        60        70        80        90       100       110       120       130         


Chain F from PDB  Type:PROTEIN  Length:137
                                                                                                                                                                         
               SCOP domains d4i3bf_ F: automated matches                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhheeeeeeeeehhhhhhhhh..hhhhhhhhhh...eeeeeee...eeeeeee.......eeeeeee....eee........eeeeeeee..eeeeeeee..eeeeeeeeee..eeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i3b F   1 MVEKFVGTWKIADSHNFGEYLKAIGAPKELSDGGDATTPTLYISQKDGDKMTVKIENGPPTFLDTQVKFKLGEEFDEFPSDRRKGVKSVVNLVGEKLVYVQKWDGKETTYVREIKDGKLVVTLTMGDVVAVRSYRRA 137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   Legend:   → Mismatch (orange background)
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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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 6)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I3B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I3B)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        UNAG_ANGJA | P0DM59: 4i3c 4i3d

(-) Related Entries Specified in the PDB File

4i3c 4i3d