Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF IRISFP IN MINERAL GREASE AT 100 K.
 
Authors :  J. P. Colletier, F. X. Gallat, N. Coquelle, M. Weik
Date :  07 Feb 16  (Deposition) - 13 Apr 16  (Release) - 13 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Colletier, M. Sliwa, F. Gallat, M. Sugahara, V. Guillon, G. Schiro, N. Coquelle, J. Woodhouse, L. Roux, G. Gotthard, A. Royant, L. M. Uriarte, C. Ruckebusch, Y. Joti, M. Byrdin, E. Mizohata, E. Nango T. Tanaka, K. Tono, M. Yabashi, V. Adam, M. Cammarata, I. Schlichting, D. Bourgeois, M. Weik
Serial Femtosecond Crystallography And Ultrafast Absorption Spectroscopy Of The Photoswitchable Fluorescent Protein Irisfp.
J. Phys. Chem. Lett. V. 7 882 2016
PubMed-ID: 26866390  |  Reference-DOI: 10.1021/ACS.JPCLETT.5B02789

(-) Compounds

Molecule 1 - GREEN TO RED PHOTOCONVERTIBLE GPF-LIKE PROTEIN EOSFP
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: LOBED BRAIN CORAL
    Organism Scientific: LOBOPHYLLIA HEMPRICHII
    Organism Taxid: 46758
    Synonym: IRISFP, GREEN TO RED PHOTOCONVERTIBLE GPF-LIKE PROTEIN EOSFP

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 27)

Asymmetric/Biological Unit (2, 27)
No.NameCountTypeFull Name
1CR84Mod. Amino Acid2-[1-AMINO-2-(1H-IMIDAZOL-5-YL)ETHYL]-1-(CARBOXYMETHYL)-4-[(4-OXOCYCLOHEXA-2,5-DIEN-1-YLIDENE)METHYL]-1H-IMIDAZOL-5-OLATE
2SO423Ligand/IonSULFATE ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:202 , LYS A:203BINDING SITE FOR RESIDUE SO4 A1224
02AC2SOFTWAREASP A:150 , HOH A:2215 , HOH A:2216 , HOH A:2219 , ALA D:167BINDING SITE FOR RESIDUE SO4 A1225
03AC3SOFTWARELYS A:85 , GLU A:181 , LYS A:182BINDING SITE FOR RESIDUE SO4 A1226
04AC4SOFTWAREASN A:17 , HIS A:22 , HOH A:2026 , HOH A:2291 , HOH A:2292 , HOH A:2293BINDING SITE FOR RESIDUE SO4 A1227
05AC5SOFTWARELYS A:182 , GLY A:183 , VAL A:184BINDING SITE FOR RESIDUE SO4 A1228
06AC6SOFTWAREGLY A:47 , HOH A:2294 , HOH A:2295BINDING SITE FOR RESIDUE SO4 A1229
07AC7SOFTWAREARG A:119 , HOH A:2174 , ASN B:17 , HIS B:22 , HIS B:121BINDING SITE FOR RESIDUE SO4 B1224
08AC8SOFTWAREGLY B:47 , HOH B:2068 , HOH B:2071 , HOH B:2248BINDING SITE FOR RESIDUE SO4 B1225
09AC9SOFTWARELYS B:134 , HOH B:2159 , HOH B:2237 , HOH B:2238 , HOH B:2249BINDING SITE FOR RESIDUE SO4 B1226
10BC1SOFTWAREALA B:167 , HOH B:2193 , HOH B:2195 , HOH B:2197 , ASP C:150 , HOH C:2165BINDING SITE FOR RESIDUE SO4 C1224
11BC2SOFTWARELYS A:37 , TYR A:211 , HOH A:2057 , HIS B:-1 , HOH B:2214 , LYS C:9 , HOH C:2207BINDING SITE FOR RESIDUE SO4 C1225
12BC3SOFTWAREASN C:17 , HIS C:22 , HIS C:121 , HOH C:2014 , HOH C:2016 , HOH C:2017 , ARG D:119BINDING SITE FOR RESIDUE SO4 C1226
13BC4SOFTWAREGLU C:46 , GLY C:47 , GLY C:48BINDING SITE FOR RESIDUE SO4 C1227
14BC5SOFTWARELYS C:182 , HOH C:2169 , HOH C:2184 , HOH C:2186 , HOH C:2208BINDING SITE FOR RESIDUE SO4 C1228
15BC6SOFTWAREASP C:202 , LYS C:203BINDING SITE FOR RESIDUE SO4 C1229
16BC7SOFTWAREALA A:167 , HOH A:2233 , HOH A:2236 , ARG D:149 , ASP D:150 , HOH D:2121 , HOH D:2154BINDING SITE FOR RESIDUE SO4 D1224
17BC8SOFTWAREARG C:119 , HOH C:2137 , ASN D:17 , HIS D:22 , HIS D:121BINDING SITE FOR RESIDUE SO4 D1225
18BC9SOFTWAREASP D:202 , LYS D:203 , HOH D:2155 , HOH D:2156BINDING SITE FOR RESIDUE SO4 D1226
19CC1SOFTWARELYS D:45 , GLU D:46 , GLY D:47 , GLY D:48 , HOH D:2041BINDING SITE FOR RESIDUE SO4 D1227
20CC2SOFTWARETYR D:211 , HOH D:2157BINDING SITE FOR RESIDUE SO4 D1228
21CC3SOFTWAREHOH C:2021 , HOH C:2141 , LYS D:178 , HOH D:2158 , HOH D:2159BINDING SITE FOR RESIDUE SO4 D1229
22CC4SOFTWARELYS D:182 , GLY D:183 , HOH D:2124BINDING SITE FOR RESIDUE SO4 D1230
23CC5SOFTWARETYR D:205 , HOH D:2106 , HOH D:2108 , HOH D:2146BINDING SITE FOR RESIDUE SO4 D1231

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FVI)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1Gly A:48 -Pro A:49
2Phe A:83 -Pro A:84
3Leu A:220 -Pro A:221
4Gly B:48 -Pro B:49
5Phe B:83 -Pro B:84
6Leu B:220 -Pro B:221
7Gly C:48 -Pro C:49
8Phe C:83 -Pro C:84
9Leu C:220 -Pro C:221
10Gly D:48 -Pro D:49
11Phe D:83 -Pro D:84
12Leu D:220 -Pro D:221

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FVI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FVI)

(-) Exons   (0, 0)

(no "Exon" information available for 5FVI)

(-) Sequences/Alignments

Asymmetric/Biological 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:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee.......hhhhhh.................hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fvi A   1 MSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFhNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDSRTTYKAKEKGVKLPGYHLVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 223
                                    10        20        30        40        50        60||      72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222 
                                                                                       61|                                                                                                                                                               
                                                                                        64-CR8                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh...............hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fvi B  -1 HHMSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFhNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDSRTTYKAKEKGVKLPGYHLVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 223
                                     8        18        28        38        48        58  ||    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
                                                                                         61|                                                                                                                                                               
                                                                                          64-CR8                                                                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeeeee..eeeeeeeeeeeehhh.eeeeeeeeee......hhhhhhhhh...............hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fvi C  -1 HHMSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFhNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDSRTTYKAKEKGVKLPGYHLVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 223
                                     8        18        28        38        48        58  ||    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
                                                                                         61|                                                                                                                                                               
                                                                                          64-CR8                                                                                                                                                           


Chain D from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeeeeeeee..eeeeeeeeeeeehhh.eeeeeeeeee.......hhhhhh.................hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5fvi D   0 HMSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFhNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDSRTTYKAKEKGVKLPGYHLVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 223
                                     9        19        29        39        49        59 ||     71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221  
                                                                                        61|                                                                                                                                                               
                                                                                         64-CR8
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5FVI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FVI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FVI)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CR8  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
    CC3  [ RasMol ]  +environment [ RasMol ]
    CC4  [ RasMol ]  +environment [ RasMol ]
    CC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:48 - Pro A:49   [ RasMol ]  
    Gly B:48 - Pro B:49   [ RasMol ]  
    Gly C:48 - Pro C:49   [ RasMol ]  
    Gly D:48 - Pro D:49   [ RasMol ]  
    Leu A:220 - Pro A:221   [ RasMol ]  
    Leu B:220 - Pro B:221   [ RasMol ]  
    Leu C:220 - Pro C:221   [ RasMol ]  
    Leu D:220 - Pro D:221   [ RasMol ]  
    Phe A:83 - Pro A:84   [ RasMol ]  
    Phe B:83 - Pro B:84   [ RasMol ]  
    Phe C:83 - Pro C:84   [ RasMol ]  
    Phe D:83 - Pro D:84   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5fvi
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q5S6Z9_LOBHE | Q5S6Z9
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q5S6Z9_LOBHE | Q5S6Z9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q5S6Z9_LOBHE | Q5S6Z9: 1zux 2btj 2vvh 2vvi 2vvj 3p8u 3s05 3tmr 3tmt 4ljb 4ljc 4ljd 4oy4 4r6b 5dtl 5fvf 5fvg

(-) Related Entries Specified in the PDB File

5fvf ROOM TEMPERATURE STRUCTURE OF IRISFP DETERMINED BY SERIAL FEMTOSECOND CRYSTALLOGRAPHY.
5fvg STRUCTURE OF IRISFP AT 100 K.