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

(-) Description

Title :  X-RAY CRYSTALLOGRAPHIC STRUCTURE OF A HIGH AFFINITY IGF2 ANTAGONIST (DOMAIN11 AB5 RHH) BASED ON HUMAN IGF2R DOMAIN 11
 
Authors :  R. D. Nicholls, C. Williams, M. Strickland, S. Frago, A. B. Hassan, M. P.
Date :  25 Feb 16  (Deposition) - 18 May 16  (Release) - 25 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Igf2, Igf2R, Domain 11, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Frago, R. D. Nicholls, M. Strickland, J. Hughes, C. Williams, L. Garner, M. Surakhy, R. Maclean, D. Rezgui, S. N. Prince, O. J. Zaccheo, D. Ebner, S. Sanegre, S. Yu, F. M. Buffa, M. P. Crump, A. B. Hassan
Functional Evolution Of Igf2:Igf2R Domain 11 Binding Generates Novel Structural Interactions And A Specific Igf2 Antagonist.
Proc. Natl. Acad. Sci. Usa V. 113 E2766 2016
PubMed-ID: 27140600  |  Reference-DOI: 10.1073/PNAS.1513023113

(-) Compounds

Molecule 1 - CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET26A
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1508-1649
    Gene: IGF2R, MPRI
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: M6PR,300 KDA MANNOSE 6-PHOSPHATE RECEPTOR,MPR 300,INSULIN- LIKE GROWTH FACTOR 2 RECEPTOR,INSULIN-LIKE GROWTH FACTOR II RECEPTOR, IGF-II RECEPTOR,M6P/IGF2 RECEPTOR,M6P/IGF2R

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION

(-) Sites  (0, 0)

(no "Site" information available for 5IEI)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:1516 -A:1553
2A:1559 -A:1566
3A:1598 -A:1634
4A:1614 -A:1646

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5IEI)

(-) 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:132
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee...eeee....eeee.hhhh....eeeee.....eee............eeeee.....eeee....eeee..eeeeee..............eeeeeeee.....eeeeee....eeeeeeeehhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5iei A 1511 NEHDDCQVTNPSTGHLFDLSSLSGRAGFTAAYAKGWGVYMSICGENENCPPGVGACFGRTRISVGKANKRLRYVDQVLQLVYKDGSHCPSKHGLSYKSVISFVCRPNRPMLISLDKQTCTLFFSWHTPLACE 1647
                                  1520      1530      1540      1550      1560      1570      1580      1590      1600      1610     |1625      1635      1645  
                                                                                                                                  1616|                         
                                                                                                                                   1622
   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 5IEI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (48, 48)

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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 5iei)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5iei)
 

(-) 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 ](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
  5iei
    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
  MPRI_HUMAN | P11717
    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
  MPRI_HUMAN | P11717
    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
        MPRI_HUMAN | P11717: 1e6f 1gp0 1gp3 1gqb 1jpl 1jwg 1lf8 2cnj 2l29 2l2a 2m68 2m6t 2v5n 2v5o 2v5p

(-) Related Entries Specified in the PDB File

1gp0 1GP0 IS THE WILD TYPE CRYSTAL STRUCTURE OF IGF2R DOMAIN 11
2l29 2L29 IS IS A NMR STRUCTURE OF A MUTANT OF DOMAIN11 OF IGF2R CONTAINING THREE MUTATIONS IN ONE OF THE LOOPS (AB) IN COMPLEX WITH MATURE HUMAN IGF2
2l2a 2L2A IS A NMR STRUCTURE OF A MUTANT OF DOMAIN11 OF IGF2R CONTAINING THREE MUTATIONS IN ONE OF THE LOOPS (AB)
2m68 2M68 IS THE NMR STRUCTURE OF A MUTANT OF DOMAIN11 OF IGF2R CONTAINING FIVE MUTATIONS IN ONE OF THE LOOPS (AB). THIS STRUCTURE IS TERMED DOMAIN11 34D OR AB5
2m6t 2M6T IS IS THE NMR STRUCTURE OF A MUTANT OF DOMAIN11 OF IGF2R CONTAINING FIVE MUTATIONS IN ONE OF THE LOOPS (AB). IN COMPLEX WITH MATURE HUMAN IGF2. THIS STRUCTURE IS TERMED DOMAIN11 34D OR AB5.