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 A CARBOHYDRATE-BINDING DOMAIN
 
Authors :  R. C. Page, C. Zheng, J. C. Nix, S. Misra, B. Zhang
Date :  13 Aug 12  (Deposition) - 05 Jun 13  (Release) - 31 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.42
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein Transport, Endoplasmic Reticulum (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Zheng, R. C. Page, V. Das, J. C. Nix, E. Wigren, S. Misra, B. Zhang
Structural Characterization Of Carbohydrate Binding By Lman Protein Provides New Insight Into The Endoplasmic Reticulum Export Of Factors V (Fv) And Viii (Fviii).
J. Biol. Chem. V. 288 20499 2013
PubMed-ID: 23709226  |  Reference-DOI: 10.1074/JBC.M113.461434

(-) Compounds

Molecule 1 - PROTEIN ERGIC-53
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: CARBOHYDRATE RECOGNITION DOMAIN UNP RESIDUES 31-270
    Gene: ERGIC53, F5F8D, LMAN1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ER-GOLGI INTERMEDIATE COMPARTMENT 53 KDA PROTEIN, GP58, INTRACELLULAR MANNOSE-SPECIFIC LECTIN MR60, LECTIN MANNOSE-BINDING 1

 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
1CA2Ligand/IonCALCIUM ION
2GOL2Ligand/IonGLYCEROL
3MAN1Ligand/IonALPHA-D-MANNOSE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:152 , PHE A:154 , ASN A:156 , ASP A:181 , HOH A:442 , HOH A:443BINDING SITE FOR RESIDUE CA A 301
2AC2SOFTWAREASP A:155 , ASP A:157 , ASN A:161 , ASN A:162 , ASP A:181 , HOH A:444BINDING SITE FOR RESIDUE CA A 302
3AC3SOFTWAREALA A:120 , ASP A:121 , PHE A:154 , ASN A:156 , HIS A:178 , GLY A:251 , GLY A:252 , LEU A:253BINDING SITE FOR RESIDUE MAN A 303
4AC4SOFTWARETHR A:97 , LYS A:98 , ALA A:100 , ASP A:226 , GLU A:228 , GLN A:241 , HOH A:471BINDING SITE FOR RESIDUE GOL A 304
5AC5SOFTWAREILE A:237 , ILE A:238 , PRO A:239 , ALA A:240 , HOH A:482BINDING SITE FOR RESIDUE GOL A 305

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:190 -A:230

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:54 -Pro A:55
2Ala A:120 -Asp A:121
3Asn A:162 -Pro A:163

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GKY)

(-) 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:229
                                                                                                                                                                                                                                                                     
               SCOP domains d4gkya_ A: automated matches                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.hhhhee.............eeeee..ee....eeee......eeeeee........eeeeeeeeee........eeeeeee................eeeeeeee...........eeeeeeee................eeee.........eeeeeeee..eeeeeee..........eeeeee.........eeeeeee......eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gky A  41 LPHRRFEYKYSFKGPHLVQSDGTVPFWAHAGNAIPSSDQIRVAPSLKSQRGSVWTKTKAAFENWEVEVTFRVTGRGRIGADGLAIWYAENQGLEGPVFGSADLWNGVGIFFDSFDNDGKKNNPAIVIIGNNGQIHYDHQNDGASQALASCQRDFRNKPYPVRAKITYYQNTLTVMINNGFTPDKNDYEFCAKVENMIIPAQGHFGISAATGGLADDHDVLSFLTFQLTE 269
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (31, 31)

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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MAN  [ 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 ]
 
  Cis Peptide Bonds
    Ala A:120 - Asp A:121   [ RasMol ]  
    Asn A:162 - Pro A:163   [ RasMol ]  
    Gly A:54 - Pro A:55   [ 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
  4gky
    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
  LMAN1_HUMAN | P49257
    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
  LMAN1_HUMAN | P49257
    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
        LMAN1_HUMAN | P49257: 3a4u 3lcp 3wht 3whu 3wnx 4gkx 4ygb 4ygc 4ygd 4yge

(-) Related Entries Specified in the PDB File

3a4u IDENTICAL PROTEIN IN THE CALCIUM-BOUND STATE, WITHOUT ALPHA -1,2-DIMANNOSE AND IN COMPLEX WITH MCDF2
3lcp IDENTICAL PROTEIN IN THE CALCIUM-BOUND STATE, WITHOUT ALPHA -1,2-DIMANNOSE AND IN COMPLEX WITH MCDF2