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 :  MENIN IN COMPLEX WITH MI-273
 
Authors :  J. Pollock, B. Dmitry, T. Cierpicki, J. Grembecka
Date :  24 Aug 15  (Deposition) - 09 Sep 15  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.66
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein Binding, Protein Binding-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Pollock, D. Borkin, G. Lund, T. Purohit, E. Dyguda-Kazimierowicz, J. Grembecka, T. Cierpicki
Rational Design Of Orthogonal Multipolar Interactions With Fluorine In Protein-Ligand Complexes.
J. Med. Chem. V. 58 7465 2015
PubMed-ID: 26288158  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B00975

(-) Compounds

Molecule 1 - MENIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-459, 537-593
    Gene: MEN1, SCG2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric/Biological Unit (5, 10)
No.NameCountTypeFull Name
15A11Ligand/Ion4-[4-(5,5-DIMETHYL-4,5-DIHYDRO-1,3-THIAZOL-2-YL)PIPERAZIN-1-YL]-6-(PENTAFLUOROETHYL)THIENO[2,3-D]PYRIMIDINE
2DMS4Ligand/IonDIMETHYL SULFOXIDE
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4PG41Ligand/IonTETRAETHYLENE GLYCOL
5SO43Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:155 , SER A:178 , GLU A:179 , ASP A:180 , HIS A:181 , ALA A:182 , PHE A:238 , CYS A:241 , TYR A:276 , MET A:278 , ASN A:282 , TYR A:319 , MET A:322 , TYR A:323 , DMS A:608 , HOH A:900 , HOH A:1068binding site for residue 5A1 A 601
02AC2SOFTWAREARG A:14 , HOH A:958 , HOH A:991binding site for residue DMS A 602
03AC3SOFTWARELEU A:75 , THR A:76 , PHE A:365 , HIS A:433 , HOH A:756 , HOH A:829 , HOH A:848 , HOH A:967 , HOH A:1126binding site for residue PG4 A 603
04AC4SOFTWARETRP A:126 , LYS A:135 , TRP A:198 , HOH A:826binding site for residue PEG A 604
05AC5SOFTWARETYR A:133 , PHE A:134 , ARG A:137 , ARG A:332binding site for residue SO4 A 605
06AC6SOFTWARELYS A:377 , ARG A:446binding site for residue SO4 A 606
07AC7SOFTWAREGLY A:190 , GLU A:191 , TYR A:227 , ARG A:229 , SER A:583binding site for residue DMS A 607
08AC8SOFTWARESER A:155 , PHE A:238 , ALA A:242 , 5A1 A:601 , HOH A:868binding site for residue DMS A 608
09AC9SOFTWAREPHE A:47 , PRO A:79 , GLY A:386 , GLN A:400 , HOH A:933binding site for residue DMS A 609
10AD1SOFTWAREARG A:332 , VAL A:334 , ARG A:335 , GLY A:401 , ALA A:403 , HOH A:761binding site for residue SO4 A 610

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:11 -Pro A:12

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DDF)

(-) 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:465
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.....hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhh.............hhhhhhhhh..hhhhhhhhhhhhhhhh.....eeee....eeeeehhhhheee................hhhhhhh.hhhhhhhh.ee.hhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh.hhhhhh..ee...ee...hhhhhhhhhhhh....hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ddf A   2 GLKAAQKTLFPLRSIDDVVRLFAAELGREEPDLVLLSLVLGFVEHFLAVNRVGLTYFPVADLSIIAALYARFTAQIRGAVDLSLYPREGGVSSRELVKKVSDVIWNSLSRSYFKDRAHIQSLFSFITGTKLDSSGVAFAVVGACQALGLRDVHLALSEDHAWVVFGPNGEQTAEVTWHGKGNEDRRGQTVNAGVAERSWLYLKGSYMRCDRKMEVAFMVCAINPSIDLHTDSLELLQLQQKLLWLLYDLGHLERYPMALGNLADLEELEPTPGRPDPLTLYHKGIASAKTYYRDEHIYPYMYLAGYHCRNRNVREALQAWADTATVIQDYNYCREDEEIYKEFFEVANDVIPNLLKEAASLLEAGSQGSALQDPECFAHLLRFYDGICKWEEGSPTPVLHVGWATFLVQSLGRFEGQVRQKVRIVSPVLTFQSEKMKGMKELLVATKINSSAIKLQLTAQSQVQM 587
                                    11        21        31        41        51 ||     81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381    || 403       413       423       433       443       453     ||552       562       572       582     
                                                                              53|                                                                                                                                                                                                                                                                                                                     386|                                                         459|                                      
                                                                               74                                                                                                                                                                                                                                                                                                                      399                                                          549
   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 5DDF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (57, 57)

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
    5A1  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DMS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PG4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
    AD1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Phe A:11 - Pro A:12   [ 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
  5ddf
    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
  MEN1_HUMAN | O00255
    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
  MEN1_HUMAN | O00255
    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
        MEN1_HUMAN | O00255: 3u84 3u85 3u86 3u88 4gpq 4gq3 4gq4 4gq6 4i80 4og3 4og4 4og5 4og6 4og7 4og8 4x5y 4x5z 5db0 5db1 5db2 5db3 5dd9 5dda 5ddb 5ddc 5ddd 5dde

(-) Related Entries Specified in the PDB File

5db0 5db1 5db2 5db3 5dd9 5dda 5ddb 5ddc 5ddd 5dde