Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE GLYCOPHORIN A TRANSMEMBRANE DIMER IN LIPIDIC CUBIC PHASE
 
Authors :  M. J. Call, M. E. Call, R. Trenker
Date :  28 Oct 15  (Deposition) - 23 Dec 15  (Release) - 06 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.81
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Receptor, Lipidic Cubic Phase, Peptides, Transmembrane, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Trenker, M. E. Call, M. J. Call
Crystal Structure Of The Glycophorin A Transmembrane Dimer In Lipidic Cubic Phase.
J. Am. Chem. Soc. V. 137 15676 2015
PubMed-ID: 26642914  |  Reference-DOI: 10.1021/JACS.5B11354

(-) Compounds

Molecule 1 - GLYCOPHORIN-A
    CellERYTHROCYTE
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTRPLE
    Expression System Taxid562
    FragmentUNP RESIDUES 89-117
    GeneGYPA, GPA
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMN SIALOGLYCOPROTEIN,PAS-2,SIALOGLYCOPROTEIN ALPHA

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1OLB1Ligand/Ion(2S)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE
2SCH4Mod. Amino AcidS-METHYL-THIO-CYSTEINE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1OLB1Ligand/Ion(2S)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE
2SCH2Mod. Amino AcidS-METHYL-THIO-CYSTEINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1OLB-1Ligand/Ion(2S)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE
2SCH2Mod. Amino AcidS-METHYL-THIO-CYSTEINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:78 , VAL B:84 , THR C:74 , VAL C:84 , ALA D:82 , LEU D:90binding site for residue OLB A 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5EH4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5EH4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EH4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EH4)

(-) Exons   (0, 0)

(no "Exon" information available for 5EH4)

(-) 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:30
                                                             
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                  5eh4 A 70 EPEITLIIFGVIAGVIGTILLISYGIRRLx 99
                                    79        89        99
                                                        99-SCH

Chain B from PDB  Type:PROTEIN  Length:30
                                                             
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                  5eh4 B 70 EPEITLIIFGVIAGVIGTILLISYGIRRLx 99
                                    79        89        99
                                                        99-SCH

Chain C from PDB  Type:PROTEIN  Length:30
                                                             
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                  5eh4 C 70 EPEITLIIFGVIAGVIGTILLISYGIRRLx 99
                                    79        89        99
                                                        99-SCH

Chain D from PDB  Type:PROTEIN  Length:30
                                                             
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                  5eh4 D 70 EPEITLIIFGVIAGVIGTILLISYGIRRLx 99
                                    79        89        99
                                                        99-SCH

   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 5EH4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EH4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EH4)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

 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
    OLB  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SCH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5eh4)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5eh4
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  GLPA_HUMAN | P02724
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  GLPA_HUMAN | P02724
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        GLPA_HUMAN | P027241afo 1msr 2kpe 2kpf 5eh6

(-) Related Entries Specified in the PDB File

5eh6