Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - model 1, sites
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - model 1, sites
NMR Structure - model 1, sites  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  BACKBONE 1H, 13C, 15N RESONANCE ASSIGNMENTS OF CALCIUM-BOUND CALMODULIN IN COMPLEX WITH PSD95 N-TERMINAL PEPTIDE
 
Authors :  Y. Zhang, J. B. Ames
Date :  26 Sep 13  (Deposition) - 24 Dec 14  (Release) - 24 Dec 14  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (10x)
NMR Structure *:  A,B  (1x)
Keywords :  Protein/Peptide, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zhang, L. Matt, T. Patriarchi, Z. A. Malik, D. Chowdhury, D. K. Park, A. Renieri, J. B. Ames, J. W. Hell
Capping Of The N-Terminus Of Psd-95 By Calmodulin Triggers Its Postsynaptic Release.
Embo J. V. 33 1341 2014
PubMed-ID: 24705785  |  Reference-DOI: 10.1002/EMBJ.201488126

(-) Compounds

Molecule 1 - CALMODULIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CALM1, CALM2
    Organism Common: CLAWED FROG,COMMON PLATANNA,PLATANNA
    Organism Scientific: XENOPUS LAEVIS
    Organism Taxid: 8355
    Synonym: CAM
 
Molecule 2 - DISKS LARGE HOMOLOG 4
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-71
    Gene: DLG4, PSD95
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: POSTSYNAPTIC DENSITY PROTEIN 95, PSD-95, SYNAPSE-ASSOCIATED PROTEIN 90, SAP-90, SAP90

 Structural Features

(-) Chains, Units

  12
NMR Structure (10x): AB
NMR Structure * (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

NMR Structure (1, 4)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
NMR Structure * (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (4, 4)

NMR Structure (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:20 , ASP A:22 , ASP A:24 , THR A:26 , GLU A:31BINDING SITE FOR RESIDUE CA A 201
2AC2SOFTWAREASP A:56 , ASP A:58 , ASN A:60 , THR A:62 , ASP A:64 , GLU A:67BINDING SITE FOR RESIDUE CA A 202
3AC3SOFTWAREASP A:93 , ASP A:95 , ASN A:97 , TYR A:99 , GLU A:104BINDING SITE FOR RESIDUE CA A 203
4AC4SOFTWAREASP A:129 , ASP A:131 , ASP A:133 , GLN A:135 , GLU A:140BINDING SITE FOR RESIDUE CA A 204

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2MES)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2MES)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2MES)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2MES)

(-) Exons   (0, 0)

(no "Exon" information available for 2MES)

(-) Sequences/Alignments

NMR Structure
   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:144
                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.........hhhhhhhhh.......hhhhhhhhhhh.........hhhhhhhhhhhh.......hhhhhhhhh......eee..hhhhhhhhh.....hhhhhhhhhh.......eeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2mes A   4 LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA 147
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143    


Chain B from PDB  Type:PROTEIN  Length:19
                                                   
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
                 Transcript ------------------- Transcript
                 2mes B   1 MDCLCIVTTKKYRYQDEDT  19
                                    10
   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 2MES)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2MES)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2MES)

(-) Gene Ontology  (75, 76)

NMR Structure(hide GO term definitions)

 Visualization

(-) Interactive Views

NMR Structure
  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 ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2mes)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - model 1, sites PNG format | NMR Structure - all models 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
  2mes
    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
  CALM1_XENLA | P0DP33
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  CAM2A_XENLA | P0DP34
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  CAM2B_XENLA | P0DP35
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  DLG4_HUMAN | P78352
    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
  CALM1_XENLA | P0DP33
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  CAM2A_XENLA | P0DP34
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  CAM2B_XENLA | P0DP35
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  DLG4_HUMAN | P78352
    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
        CALM1_XENLA | P0DP33: 1aji 1cfc 1cfd 1cff 1ckk 1cm1 1cm4 1deg 1dmo 1f70 1f71 1iq5 1k90 1k93 1lvc 1mux 1nkf 1nwd 1qiv 1qiw 1sk6 1sy9 1up5 1x02 1y0v 2col 2i08 2k3s 2kdu 2llo 2llq 2rrt 3cln 4r8g 5t0x
        CAM2A_XENLA | P0DP34: 1aji 1cfc 1cfd 1cff 1ckk 1cm1 1cm4 1deg 1dmo 1f70 1f71 1iq5 1k90 1k93 1lvc 1mux 1nkf 1nwd 1qiv 1qiw 1sk6 1sy9 1up5 1x02 1y0v 2col 2i08 2k3s 2kdu 2llo 2llq 2rrt 3cln 4r8g 5t0x
        CAM2B_XENLA | P0DP35: 1aji 1cfc 1cfd 1cff 1ckk 1cm1 1cm4 1deg 1dmo 1f70 1f71 1iq5 1k90 1k93 1lvc 1mux 1nkf 1nwd 1qiv 1qiw 1sk6 1sy9 1up5 1x02 1y0v 2col 2i08 2k3s 2kdu 2llo 2llq 2rrt 3cln 4r8g 5t0x
        DLG4_HUMAN | P78352: 1kef 3i4w 3k82 3zrt 5jxb

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2MES)