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 :  THE CRYSTAL STRUCTURE OF LIGHT-DRIVEN CHLORIDE PUMP CLR (T102N) MUTANT AT PH 4.5.
 
Authors :  K. L. Kim, S. K. Kwon, S. H. Jun, J. S. Cha, H. Y. Kim, J. H. Kim, H. S. Cho
Date :  07 Apr 16  (Deposition) - 19 Oct 16  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Kim, S. Kwon, S. Jun, J. S. Cha, H. Kim, W. Lee, J. F. Kim, H. Cho
Crystal Structure And Functional Characterization Of A Light-Driven Chloride Pump Having An Ntq Motif.
Nat. Commun. V. 7 12677 2016
PubMed-ID: 27554809  |  Reference-DOI: 10.1038/NCOMMS12677

(-) Compounds

Molecule 1 - CHLORIDE PUMP RHODOPSIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET VECTOR
    Fragment: SEVEN TRANS-MEMBRANE
    Mutation: YES
    Organism Scientific: NONLABENS MARINUS S1-08
    Organism Taxid: 1454201

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2OLA8Ligand/IonOLEIC ACID
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4RET1Ligand/IonRETINAL

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:80 , GLU A:120 , THR A:124 , LYS A:174BINDING SITE FOR RESIDUE OLA A 1266
02AC2SOFTWARETYR A:244BINDING SITE FOR RESIDUE OLA A 1267
03AC3SOFTWAREGLN A:41BINDING SITE FOR RESIDUE OLA A 1268
04AC4SOFTWAREGLY A:118 , LEU A:121 , PHE A:122 , THR A:126 , ILE A:129BINDING SITE FOR RESIDUE OLA A 1270
05AC5SOFTWAREGLN A:152 , TRP A:156 , TRP A:195 , PHE A:199BINDING SITE FOR RESIDUE OLA A 1271
06AC6SOFTWAREVAL A:165 , ILE A:232 , HOH A:2016 , HOH A:2086BINDING SITE FOR RESIDUE OLA A 1272
07AC7SOFTWAREMET A:154 , THR A:161 , TYR A:244BINDING SITE FOR RESIDUE OLA A 1273
08AC8SOFTWARETRP A:99 , ILE A:103 , LEU A:106 , MET A:135 , SER A:160 , PHE A:164 , TRP A:201 , TYR A:204 , TYR A:208 , SER A:234 , LYS A:235BINDING SITE FOR RESIDUE RET A 1274
09AC9SOFTWAREGLY A:185 , ASP A:187BINDING SITE FOR RESIDUE PEG A 1275
10BC1SOFTWAREASN A:98 , TRP A:99 , ASN A:102 , LYS A:235BINDING SITE FOR RESIDUE CL A 1276
11BC2SOFTWAREPRO A:45 , LYS A:46BINDING SITE FOR RESIDUE CL A 1277

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5G2D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5G2D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5G2D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5G2D)

(-) Exons   (0, 0)

(no "Exon" information available for 5G2D)

(-) 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:267
                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhheeee..eeee......hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5g2d A  -1 NSMKNIESLFDYSAGQFEFIDHLLTMGVGVHFAALIFFLVVSQFVAPKYRIATALSCIVMVSAGLILNSQAVMWTDAYAYVDGSYQLQDLTFSNGYRYVNWMANIPCLLLQLLIVLNLKGKELFSTATWLILAAWGMIITGYVGQLYEVDDIAQLMIWGAVSTAFFVVMNWIVGTKIFKNRATMLGGTDSTITKVFWLMMFAWTLYPIAYLVPAFMNNADGVVLRQLLFTIADISSKVIYGLMITYIAIQQSAAAGYVPAQQALGRI 265
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258
   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 5G2D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5G2D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5G2D)

(-) Gene Ontology  (5, 5)

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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OLA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    RET  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5g2d)
 

(-) 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
  5g2d
    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
  W8VZW3_9FLAO | W8VZW3
    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
  W8VZW3_9FLAO | W8VZW3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        W8VZW3_9FLAO | W8VZW3: 5b2n 5fjg 5g28 5g2a 5g2c 5g54

(-) Related Entries Specified in the PDB File

5g28 THE CRYSTAL STRUCTURE OF LIGHT-DRIVEN CHLORIDE PUMP CLR AT PH 6.0.
5g29 THE CRYSTAL STRUCTURE OF LIGHT-DRIVEN CHLORIDE PUMP CLR AT PH 4.5.
5g2a THE CRYSTAL STRUCTURE OF LIGHT-DRIVEN CHLORIDE PUMP CLR AT PH 6.0 WITH BROMIDE ION.
5g2c THE CRYSTAL STRUCTURE OF LIGHT-DRIVEN CHLORIDE PUMP CLR (T102D) MUTANT AT PH 6.0.