Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  FMO PROTEIN FROM PROSTHECOCHLORIS AESTUARII 2K AT ROOM TEMPERATURE
 
Authors :  D. E. Tronrud, B. W. Matthews
Date :  17 Apr 98  (Deposition) - 16 Sep 98  (Release) - 18 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Electron Transport, Excitation Energy Transfer, Reaction Center (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. E. Tronrud, B. W. Matthews
Refinement Of The Structure Of A Water-Soluble Antenna Complex From Green Photosynthetic Bacteria By Incorporation Of The Chemically Determined Amino Acid Sequence
Photosynthetic Reaction V. 1 13 1993 Center
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BACTERIOCHLOROPHYLL A PROTEIN
    Cellular Location: LIGHT GATHERING ANTENNA COMPLEX
    Chains: A
    Organism Scientific: PROSTHECOCHLORIS AESTUARII
    Organism Taxid: 1102
    Synonym: FENNA-MATTHEWS-OLSON PROTEIN, FMO-PROTEIN, BCHL A PROTEIN, BCP

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric Unit (1, 7)
No.NameCountTypeFull Name
1BCL7Ligand/IonBACTERIOCHLOROPHYLL A
Biological Unit 1 (1, 21)
No.NameCountTypeFull Name
1BCL21Ligand/IonBACTERIOCHLOROPHYLL A

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:103 , PHE A:108 , HIS A:110 , PHE A:112 , SER A:126 , VAL A:129 , MET A:149 , VAL A:151 , LEU A:158 , THR A:161 , TRP A:162 , PHE A:165 , TRP A:184 , VAL A:205 , BCL A:368 , BCL A:372 , HOH A:463BINDING SITE FOR RESIDUE BCL A 367
2AC2SOFTWAREILE A:52 , PHE A:66 , VAL A:85 , ARG A:95 , ILE A:96 , ALA A:97 , VAL A:118 , GLN A:143 , HIS A:145 , TRP A:184 , HIS A:227 , SER A:235 , TRP A:239 , SER A:253 , BCL A:367 , BCL A:370 , BCL A:371 , BCL A:373BINDING SITE FOR RESIDUE BCL A 368
3AC3SOFTWARETYR A:15 , ILE A:17 , LEU A:288 , HIS A:290 , PRO A:291 , PRO A:294 , HIS A:298 , TYR A:345 , TRP A:348 , PHE A:360 , BCL A:371 , BCL A:373 , HOH A:394BINDING SITE FOR RESIDUE BCL A 369
4AC4SOFTWAREALA A:40 , TYR A:138 , ILE A:186 , PRO A:188 , ALA A:189 , GLN A:198 , ILE A:293 , HIS A:297 , HIS A:298 , MET A:300 , VAL A:301 , BCL A:368 , BCL A:371 , BCL A:372 , BCL A:373 , HOH A:408BINDING SITE FOR RESIDUE BCL A 370
5AC5SOFTWAREALA A:11 , TYR A:15 , ALA A:33 , PRO A:38 , ALA A:39 , ALA A:40 , ILE A:41 , PHE A:258 , SER A:260 , ILE A:265 , HIS A:298 , VAL A:301 , GLY A:302 , ASN A:305 , BCL A:368 , BCL A:369 , BCL A:370 , BCL A:373 , HOH A:471BINDING SITE FOR RESIDUE BCL A 371
6AC6SOFTWARESER A:72 , VAL A:74 , ASN A:79 , VAL A:105 , PHE A:114 , VAL A:129 , ILE A:133 , PRO A:136 , ILE A:137 , TYR A:138 , GLN A:140 , PHE A:183 , TRP A:184 , ILE A:186 , BCL A:367 , BCL A:370 , HOH A:386 , HOH A:421BINDING SITE FOR RESIDUE BCL A 372
7AC7SOFTWAREALA A:54 , VAL A:64 , PHE A:66 , SER A:235 , ARG A:238 , LEU A:242 , PHE A:243 , PRO A:244 , PRO A:291 , BCL A:368 , BCL A:369 , BCL A:370 , BCL A:371 , HOH A:406BINDING SITE FOR RESIDUE BCL A 373

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:44 -Pro A:45
2Ala A:327 -Pro A:328

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4BCL)

(-) 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:350
 aligned with BCPA_PROAE | P11741 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:359
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357         
           BCPA_PROAE     8 TTTAHSDYEIILEGGSSSWGQVKGRAKVNVPAAIPLLPTDCNIRIDAKPLDAQKGVVRFTTKIESVVDSVKNTLNVEVDIANETKDRRIAVGEGSLSVGDFSHSFSFEGQVVNMYYYRSDAVRRNIPNPIYMQGRQFHDILMKVPLDNNDLVDTWEGFQQSISGGGANFGDWIREFWFIGPAFAAINEGGQRISPIVVNSSNVEGGEKGPVGVTRWKFSHAGSGVVDSISRWTELFPVEQLNKPASIEGGFRSDSQGIEVKVDGNLPGVSRDAGGGLRRILNHPLIPLVHHGMVGKFNDFTVDTQLKIVLPKGYKIRYAAPQFRSQNLEEYRWSGGAYARWVEHVCKGGTGQFEVLYAQ 366
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 4bclA00 A:8-366 Bacteriochlorophyll-a Protein                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee.......eeeeeeeee..........eeeeeeeeeeeee---.eeeeeeeeeeee..eeeeeeeeeeeee....eeeeeeeeeeee..eeeeeeeeeeeeeee....hhhh..........eeeeeeeeeeee...hhhhhhhhhhhhh.---...hhhhhhhhh..hhhhhhhhh..eee...eeeeeeee.---..eeeeeeeeeeee....hhhh.......hhh....eeeeeeeee....eeeeeeeee...eeeee..eeee....hhhhhhhhh.......eeeeeeeee.....eeeeee....eee..eeeee.hhhhhhhhhhhh......eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bcl A   8 TTTAHSDYEIILEGGSSSWGQVKGRAKVNVPAAIPLLPTDCNIRIDAKPLD---GVVRFTTKIESVVDSVKNTLNVEVDIANETKDRRIAVGEGSLSVGDFSHSFSFEGSVVNMYYYRSDAVRRNIPNPIYMQGRQFHDILMKVPLDNNDLVDTWEGFQQSI---GANFGDWIREFWFIGPAFAAINEGGQRISPIVVNSSNVEG---GPVGVTRWKFSHAGSGVVDSISRWTELFPVEQLNKPASIEGGFRSDSQGIEVKVDGNLPGVSRDAGGGLRRILNHPLIPLVHHGMVGKFNDFTVDTQLKIVLPKGYKIRYAAPQFRSQNLEEYRWSGGAYARWVEHVCKGGTGQFEVLYAQ 366
                                    17        27        37        47        57|   |   67        77        87        97       107       117       127       137       147       157       167 |   | 177       187       197       207    |  217       227       237       247       257       267       277       287       297       307       317       327       337       347       357         
                                                                             58  62                                                                                                        169 173                                    212 216
   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 4BCL)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (BCPA_PROAE | P11741)
molecular function
    GO:0042314    bacteriochlorophyll binding    Interacting selectively and non-covalently with bacteriochlorophyll, a form of chlorophyll found in photosynthetic bacteria, such as the purple and green bacteria. There are several types, designated a to g. Bacteriochlorophyll a and bacteriochlorophyll b are structurally similar to the chlorophyll a and chlorophyll b found in plants.
    GO:0016168    chlorophyll binding    Interacting selectively and non-covalently with chlorophyll; any compound of magnesium complexed in a porphyrin (tetrapyrrole) ring and which functions as a photosynthetic pigment.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0015979    photosynthesis    The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.

 Visualization

(-) Interactive Views

Asymmetric 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
    BCL  [ 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 ]
 
  Cis Peptide Bonds
    Ala A:327 - Pro A:328   [ RasMol ]  
    Leu A:44 - Pro A:45   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  4bcl
    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
  BCPA_PROAE | P11741
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  BCPA_PROAE | P11741
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        BCPA_PROAE | P11741: 3eoj

(-) Related Entries Specified in the PDB File

3eoj