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 :  CRYSTAL STRUCTURE OF GLTPH L66C-S300C MUTANT CROSSLINKED WITH DIVALENT MERCURY
 
Authors :  N. Reyes, O. Boudker
Date :  30 Jan 13  (Deposition) - 10 Apr 13  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.50
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Amino Acid Transport System X-Ag, Biological Transport, Structure- Activity Relationship, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Reyes, S. Oh, O. Boudker
Binding Thermodynamics Of A Glutamate Transporter Homolog.
Nat. Struct. Mol. Biol. V. 20 634 2013
PubMed-ID: 23563139  |  Reference-DOI: 10.1038/NSMB.2548

(-) Compounds

Molecule 1 - 425AA LONG HYPOTHETICAL PROTON GLUTAMATE SYMPORT PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD24
    Expression System Strain: TOP10
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RERSIDUES 1-417
    Gene: PH1295
    Mutation: YES
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: ATCC 700860

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1ASP3Mod. Amino AcidASPARTIC ACID
2HG3Ligand/IonMERCURY (II) ION
3NA6Ligand/IonSODIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:308 , MET A:311 , SER A:349 , ILE A:350 , THR A:352BINDING SITE FOR RESIDUE NA A 501
02AC2SOFTWAREGLY A:306 , ASN A:310 , ASN A:401 , ASP A:405BINDING SITE FOR RESIDUE NA A 502
03AC3SOFTWAREARG A:276 , SER A:277 , SER A:278 , MET A:311 , THR A:314 , GLY A:354 , PRO A:356 , ALA A:358 , GLY A:359 , ASP A:394 , ARG A:397 , THR A:398 , ASN A:401BINDING SITE FOR RESIDUE ASP A 503
04AC4SOFTWARECYS A:66 , CYS A:300BINDING SITE FOR RESIDUE HG A 504
05AC5SOFTWARETHR B:308 , MET B:311 , SER B:349 , ILE B:350 , THR B:352BINDING SITE FOR RESIDUE NA B 501
06AC6SOFTWAREGLY B:306 , ASN B:310 , ASN B:401 , ASP B:405BINDING SITE FOR RESIDUE NA B 502
07AC7SOFTWAREARG B:276 , SER B:278 , MET B:311 , THR B:314 , THR B:352 , GLY B:354 , VAL B:355 , PRO B:356 , GLY B:357 , ALA B:358 , GLY B:359 , ASP B:394 , ARG B:397 , THR B:398 , ASN B:401BINDING SITE FOR RESIDUE ASP B 503
08AC8SOFTWARECYS B:66 , ILE B:159 , CYS B:300BINDING SITE FOR RESIDUE HG B 504
09AC9SOFTWARETHR C:308 , MET C:311 , SER C:349 , ILE C:350 , THR C:352BINDING SITE FOR RESIDUE NA C 501
10BC1SOFTWAREGLY C:306 , ASN C:310 , ASN C:401 , ASP C:405BINDING SITE FOR RESIDUE NA C 502
11BC2SOFTWAREARG C:276 , SER C:277 , SER C:278 , MET C:311 , THR C:314 , ALA C:353 , GLY C:354 , GLY C:357 , ALA C:358 , GLY C:359 , ASP C:394 , ARG C:397 , THR C:398 , ASN C:401BINDING SITE FOR RESIDUE ASP C 503
12BC3SOFTWARECYS C:66 , GLY C:69BINDING SITE FOR RESIDUE HG C 504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ala A:127 -Pro A:128
2Ala B:127 -Pro B:128
3Ala C:127 -Pro C:128

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IZM)

(-) 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:404
                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhh...........hhhhhhhhhhhhhhhhhhhhhhh...................................hhhhhh.....hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh......hhhhhhhhhhhhhhh......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4izm A  13 LQKILIGLILGAIVGLILGHYGYAHAVHTYVKPFGDLFVRLLKMLVMPIVFASCVVGAASISPARLGRVGVKIVVYYLLTSAFAVTLGIIMARLFNPGAGIHLAVGGQQFQPHQAPPLVHILLDIVPTNPFGALANGQVLPTIFFAIILGIAITYLMNSENEKVRKSAETLLDAINGLAEAMYKIVNGVMQYAPIGVFALIAYVMAEQGVHVVGELAKVTAAVYVGLTLQILLVYFVLLKIYGIDPISFIKHAKDAMLTAFVTRSSSGTLPVTMRVAKEMGISEGIYCFTLPLGATINMDGTALYQGVATFFIANALGSHLTVGQQLTIVLTAVLASIGTAGVPGAGAIMLAMVLHSVGLPLTDPNVAAAYAMILGIDAILDMGRTMVNVTGDLTGTAIVAKTE 416
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412    


Chain B from PDB  Type:PROTEIN  Length:404
                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh...........................hhhhhh.....hhhhhh......hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh....hhhhhh...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhh...........hhhhhhhhhh.......hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4izm B  13 LQKILIGLILGAIVGLILGHYGYAHAVHTYVKPFGDLFVRLLKMLVMPIVFASCVVGAASISPARLGRVGVKIVVYYLLTSAFAVTLGIIMARLFNPGAGIHLAVGGQQFQPHQAPPLVHILLDIVPTNPFGALANGQVLPTIFFAIILGIAITYLMNSENEKVRKSAETLLDAINGLAEAMYKIVNGVMQYAPIGVFALIAYVMAEQGVHVVGELAKVTAAVYVGLTLQILLVYFVLLKIYGIDPISFIKHAKDAMLTAFVTRSSSGTLPVTMRVAKEMGISEGIYCFTLPLGATINMDGTALYQGVATFFIANALGSHLTVGQQLTIVLTAVLASIGTAGVPGAGAIMLAMVLHSVGLPLTDPNVAAAYAMILGIDAILDMGRTMVNVTGDLTGTAIVAKTE 416
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412    


Chain C from PDB  Type:PROTEIN  Length:404
                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.hhhhh..........hhhhhhhhhhhhhhhhhhhhh.hhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh.........................hhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh......hhhhhhhhhhh...hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhh......hhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4izm C  13 LQKILIGLILGAIVGLILGHYGYAHAVHTYVKPFGDLFVRLLKMLVMPIVFASCVVGAASISPARLGRVGVKIVVYYLLTSAFAVTLGIIMARLFNPGAGIHLAVGGQQFQPHQAPPLVHILLDIVPTNPFGALANGQVLPTIFFAIILGIAITYLMNSENEKVRKSAETLLDAINGLAEAMYKIVNGVMQYAPIGVFALIAYVMAEQGVHVVGELAKVTAAVYVGLTLQILLVYFVLLKIYGIDPISFIKHAKDAMLTAFVTRSSSGTLPVTMRVAKEMGISEGIYCFTLPLGATINMDGTALYQGVATFFIANALGSHLTVGQQLTIVLTAVLASIGTAGVPGAGAIMLAMVLHSVGLPLTDPNVAAAYAMILGIDAILDMGRTMVNVTGDLTGTAIVAKTE 416
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412
   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 4IZM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

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
    ASP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ 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 ]
 
  Cis Peptide Bonds
    Ala A:127 - Pro A:128   [ RasMol ]  
    Ala B:127 - Pro B:128   [ RasMol ]  
    Ala C:127 - Pro C:128   [ 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
  4izm
    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
  O59010_PYRHO | O59010
    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
  O59010_PYRHO | O59010
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        O59010_PYRHO | O59010: 1xfh 2nwl 2nww 2nwx 3kbc 3v8f 3v8g 4oye 4oyf 4p19 4p1a 4p3j 4p6h 4x2s 5cfy

(-) Related Entries Specified in the PDB File

2nwl CRYSTAL STRUCTURE OF GLTPH IN COMPLEX WITH L-ASP
2nww CRYSTAL STRUCTURE OF GLTPH IN COMPLEX WITH TBOA
2nwx CRYSTAL STRUCTURE OF GLTPH IN COMPLEX WITH L-ASPARTATE AND SODIUM IONS
3kbc CRYSTAL STRUCTURE OF GLTPH K55C-A364C MUTANT CROSSLINKED WITH DIVALENT MERCURY
3v8f CRYSTAL STRUCTURE OF CROSSLINKED GLTPH V216C-M385C MUTANT
3v8g CRYSTAL STRUCTURE OF AN ASYMMETRIC TRIMER OF A GLUTAMATE TRANSPORTER HOMOLOGUE (GLTPH)