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 :  X-RAY STRUCTURE OF THE AMYLOID PRECURSOR PROTEIN-LIKE PROTEIN 1 (APLP1) E2 DOMAIN IN COMPLEX WITH A HEPARIN DODECASACCHARIDE
 
Authors :  S. O. Dahms, M. E. Than
Date :  18 Sep 14  (Deposition) - 11 Mar 15  (Release) - 18 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Heparan Sulfate Binding, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. O. Dahms, M. C. Mayer, D. Roeser, G. Multhaup, M. E. Than
Interaction Of The Amyloid Precursor Protein-Like Protein 1 (Aplp1) E2 Domain With Heparan Sulfate Involves Two Distinc Binding Modes.
Acta Crystallogr. , Sect. D V. 71 494 2015
PubMed-ID: 25760599  |  Reference-DOI: 10.1107/S1399004714027114

(-) Compounds

Molecule 1 - AMYLOID-LIKE PROTEIN 1
    ChainsA, B
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System Taxid4922
    FragmentE2 DOMAIN, UNP RESIDUES 292-494
    GeneAPLP1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAPLP, APLP-1, C30

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
1IDS5Ligand/Ion2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID
2SGN5Ligand/IonN,O6-DISULFO-GLUCOSAMINE
3UAP1Ligand/Ion4-DEOXY-2-O-SULFO-ALPHA-L-THREO-HEX-4-ENOPYRANURONICACID
4ZN1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:310 , LYS A:314 , ARG A:369 , VAL A:373 , HIS A:433 , SGN A:502 , HOH A:623 , HOH A:643 , HOH A:644 , HOH A:645 , HIS B:433 , SGN B:501BINDING SITE FOR RESIDUE UAP A 501
02AC2SOFTWAREHIS A:426 , ARG A:429 , HIS A:430 , HIS A:433 , UAP A:501 , IDS A:503 , HOH A:643 , LYS B:314 , ARG B:369BINDING SITE FOR RESIDUE SGN A 502
03AC3SOFTWAREHIS A:307 , HIS A:376 , VAL A:380 , HIS A:426 , ARG A:429 , SGN A:502 , SGN A:504BINDING SITE FOR RESIDUE IDS A 503
04AC4SOFTWAREHIS A:307 , HIS A:376 , VAL A:380 , IDS A:503 , IDS A:505BINDING SITE FOR RESIDUE SGN A 504
05AC5SOFTWARESGN A:504BINDING SITE FOR RESIDUE IDS A 505
06AC6SOFTWAREHIS A:486 , HOH A:602 , HOH A:609 , HOH A:611 , HOH A:613BINDING SITE FOR RESIDUE ZN A 506
07AC7SOFTWARELYS A:314 , UAP A:501 , ARG B:429 , HIS B:430 , HIS B:433 , IDS B:502 , HOH B:622 , HOH B:623BINDING SITE FOR RESIDUE SGN B 501
08AC8SOFTWAREHIS B:376 , HIS B:426 , ARG B:429 , SGN B:501 , SGN B:503 , HOH B:623BINDING SITE FOR RESIDUE IDS B 502
09AC9SOFTWAREHIS B:307 , HIS B:376 , VAL B:380 , IDS B:502 , IDS B:504BINDING SITE FOR RESIDUE SGN B 503
10BC1SOFTWARESGN B:503 , SGN B:505BINDING SITE FOR RESIDUE IDS B 504
11BC2SOFTWAREARG B:418 , IDS B:504 , IDS B:506BINDING SITE FOR RESIDUE SGN B 505
12BC3SOFTWAREARG B:415 , SGN B:505BINDING SITE FOR RESIDUE IDS B 506

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asp A:402 -Pro A:403
2Asp B:402 -Pro B:403

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RDA)

(-) 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:203
                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rda A 292 DGVDIYFGMPGEISEHEGFLRAKMDLEERRMRQINEVMREWAMADNQSKNLPKADRQALNEHFQSILQTLEEQVSGERQRLVETHATRVIALINDQRRAALEGFLAALQADPPQAERVLLALRRYLRAEQKEQRHTLRHYQHVAAVDPEKAQQMRFQVHTHLQVIEERVNQSLGLLDQNPHLAQELRPQIQELLHSEHLGPSE 494
                                   301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491   

Chain B from PDB  Type:PROTEIN  Length:196
                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rda B 292 DGVDIYFGMPGEISEHEGFLRAKMDLEERRMRQINEVMREWAMADNQSKNLPKADRQALNEHFQSILQTLEEQVSGERQRLVETHATRVIALINDQRRAALEGFLAALQADPPQAERVLLALRRYLRAEQKEQRHTLRHYQHVAAVDPEKAQQMRFQVHTHLQVIEERVNQSLGLLDQNPHLAQELRPQIQELLHS 487
                                   301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481      

   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 4RDA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

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
    IDS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SGN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UAP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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
    Asp A:402 - Pro A:403   [ RasMol ]  
    Asp B:402 - Pro B:403   [ RasMol ]  
 

(-) 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
  4rda
    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
  APLP1_HUMAN | P51693
    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
  APLP1_HUMAN | P51693
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        APLP1_HUMAN | P516933pmr 3q7g 3q7l 3qmk 4rd9

(-) Related Entries Specified in the PDB File

4rd9