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(-) Description

Title :  PADRON0.9-ON (FLUORESCENT STATE)
 
Authors :  T. Brakemann, G. Weber, S. Trowitzsch, M. C. Wahl, S. Jakobs
Date :  12 Feb 10  (Deposition) - 16 Mar 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
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 :  Beta-Barrel, Cis-Trans Isomerisation, Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Brakemann, G. Weber, M. Andresen, G. Groenhof, A. C. Stiel, S. Trowitzsch, C. Eggeling, H. Grubmuller, S. W. Hell, M. C. Wahl, S. Jakobs
Molecular Basis Of The Light-Driven Switching Of The Photochromic Fluorescent Protein Padron.
J. Biol. Chem. V. 285 14603 2010
PubMed-ID: 20236929  |  Reference-DOI: 10.1074/JBC.M109.086314

(-) Compounds

Molecule 1 - PADRON0.9
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: PECTINIIDAE
    Organism Taxid: 46733

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
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)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric Unit (4, 15)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2GOL5Ligand/IonGLYCEROL
3GYC4Mod. Amino Acid[(4Z)-2-[(1R)-1-AMINO-2-MERCAPTOETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
4SPD5Ligand/IonSPERMIDINE
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1EPE-1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2GOL2Ligand/IonGLYCEROL
3GYC1Mod. Amino Acid[(4Z)-2-[(1R)-1-AMINO-2-MERCAPTOETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
4SPD1Ligand/IonSPERMIDINE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1EPE-1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2GOL-1Ligand/IonGLYCEROL
3GYC1Mod. Amino Acid[(4Z)-2-[(1R)-1-AMINO-2-MERCAPTOETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
4SPD2Ligand/IonSPERMIDINE
Biological Unit 3 (3, 4)
No.NameCountTypeFull Name
1EPE-1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2GOL1Ligand/IonGLYCEROL
3GYC1Mod. Amino Acid[(4Z)-2-[(1R)-1-AMINO-2-MERCAPTOETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
4SPD2Ligand/IonSPERMIDINE
Biological Unit 4 (3, 4)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2GOL2Ligand/IonGLYCEROL
3GYC1Mod. Amino Acid[(4Z)-2-[(1R)-1-AMINO-2-MERCAPTOETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
4SPD-1Ligand/IonSPERMIDINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS C:21 , PRO C:51 , ARG C:149 , ASP C:150 , GLY D:165 , GLY D:167 , HOH D:274 , HOH D:289BINDING SITE FOR RESIDUE EPE D 225
02AC2SOFTWARELYS A:11 , ILE A:115 , ILE D:198BINDING SITE FOR RESIDUE GOL A 225
03AC3SOFTWAREILE A:100 , SPD A:227BINDING SITE FOR RESIDUE GOL A 226
04AC4SOFTWARESER C:199 , HIS C:200 , ASP C:201 , ASN C:206 , VAL C:207 , ASN C:208 , HOH C:433BINDING SITE FOR RESIDUE GOL C 225
05AC5SOFTWAREILE D:94 , TYR D:95 , GLU D:96 , ARG D:170 , ASP D:172 , HOH D:239BINDING SITE FOR RESIDUE GOL D 226
06AC6SOFTWARESER D:199 , ASN D:206 , VAL D:207 , ASN D:208 , HOH D:591 , HOH D:640BINDING SITE FOR RESIDUE GOL D 227
07AC7SOFTWARELYS A:174 , ILE B:94 , GLU B:96 , ARG B:170 , ASP B:172 , ASP C:97BINDING SITE FOR RESIDUE SPD B 225
08AC8SOFTWAREILE A:94 , GLU A:96 , ARG A:170 , ASP A:172 , GOL A:226 , TYR B:147 , ASP B:156 , LYS B:174BINDING SITE FOR RESIDUE SPD A 227
09AC9SOFTWAREASP B:150 , GLY B:151 , ALA B:179 , LYS B:180 , LYS B:181 , LYS C:43 , ASN C:206BINDING SITE FOR RESIDUE SPD B 226
10BC1SOFTWAREPRO C:49 , LEU C:50 , PRO C:51 , LYS C:134BINDING SITE FOR RESIDUE SPD C 226
11BC2SOFTWAREASP C:97 , GLY C:129 , PRO C:130 , HIS C:168 , HOH C:381 , ARG D:149BINDING SITE FOR RESIDUE SPD C 227

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LS3)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Gly A:48 -Pro A:49
2Phe A:83 -Pro A:84
3Gly B:48 -Pro B:49
4Phe B:83 -Pro B:84
5Gly C:48 -Pro C:49
6Phe C:83 -Pro C:84
7Gly D:48 -Pro D:49
8Phe D:83 -Pro D:84

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LS3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LS3)

(-) Exons   (0, 0)

(no "Exon" information available for 3LS3)

(-) 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:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhh.................hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ls3 A   1 MSVIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTMAFcNRVFAKYPENIVDYFKQSFPEGYSWERSMIYEDGGICNATNDITLDGDCYICEIRFDGVNFPANGPVMQKRTVKWELSTEKLYVRDGVLKSDGNYALSLEGGGHYRCDFKTTYKAKKVVQLPDYHSVDHHIEIISHDKDYSNVNLHEHAEAHSE 218
                                    10        20        30        40        50        60 ||     72        82        92       102       112       122       132       142       152       162       172       182       192       202       212      
                                                                                        62-GYC                                                                                                                                                      
                                                                                         65                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhh.................hhhhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ls3 B   2 SVIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTMAFcNRVFAKYPENIVDYFKQSFPEGYSWERSMIYEDGGICNATNDITLDGDCYICEIRFDGVNFPANGPVMQKRTVKWELSTEKLYVRDGVLKSDGNYALSLEGGGHYRCDFKTTYKAKKVVQLPDYHSVDHHIEIISHDKDYSNVNLHEHAEAHSE 218
                                    11        21        31        41        51        61||      73        83        93       103       113       123       133       143       153       163       173       183       193       203       213     
                                                                                       62-GYC                                                                                                                                                      
                                                                                        65                                                                                                                                                         


Chain C from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhh................hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ls3 C   2 SVIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTMAFcNRVFAKYPENIVDYFKQSFPEGYSWERSMIYEDGGICNATNDITLDGDCYICEIRFDGVNFPANGPVMQKRTVKWELSTEKLYVRDGVLKSDGNYALSLEGGGHYRCDFKTTYKAKKVVQLPDYHSVDHHIEIISHDKDYSNVNLHEHAEAHS 217
                                    11        21        31        41        51        61||      73        83        93       103       113       123       133       143       153       163       173       183       193       203       213    
                                                                                       62-GYC                                                                                                                                                     
                                                                                        65                                                                                                                                                        


Chain D from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.........eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhh................hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ls3 D  -8 HHHHHHTDPMSVIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTMAFcNRVFAKYPENIVDYFKQSFPEGYSWERSMIYEDGGICNATNDITLDGDCYICEIRFDGVNFPANGPVMQKRTVKWELSTEKLYVRDGVLKSDGNYALSLEGGGHYRCDFKTTYKAKKVVQLPDYHSVDHHIEIISHDKDYSNVNLHEHAEAHSE 218
                                     1        11        21        31        41        51        61||      73        83        93       103       113       123       133       143       153       163       173       183       193       203       213     
                                                                                                 62-GYC                                                                                                                                                      
                                                                                                  65
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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  (0, 0)

(no "SCOP Domain" information available for 3LS3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LS3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3LS3)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3LS3)

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3lsa