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 :  MIF IN COMPLEX WITH 4-[(4-OXO-2-THIOXO-1,3-THIAZOLAN-3-YL) METHYL]BENZONITRILE
 
Authors :  T. Y. Cho
Date :  27 Mar 15  (Deposition) - 28 Sep 16  (Release) - 04 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Covalent Inhibitor, Protein Surface Modification, Isomerase-Isomerase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. K. Singh, G. Pantouris, S. Borosch, S. Rojanasthien, T. Y. Cho
Structural Basis For Decreased Induction Of Class Ib Pi3-Kinases Expression By Mif Inhibitors.
J. Cell. Mol. Med. V. 21 142 2017
PubMed-ID: 27619729  |  Reference-DOI: 10.1111/JCMM.12949

(-) Compounds

Molecule 1 - MACROPHAGE MIGRATION INHIBITORY FACTOR
    Chains: A, B, C
    EC Number: 5.3.2.1, 5.3.3.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: MIF, GLIF, MMIF
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MIF,GLYCOSYLATION-INHIBITING FACTOR,GIF,L-DOPACHROME ISOMERASE,L-DOPACHROME TAUTOMERASE,PHENYLPYRUVATE TAUTOMERASE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
14N93Mod. Amino Acid1-[(4-CYANOBENZYL)CARBAMOTHIOYL]-L-PROLINE
2IPA2Ligand/IonISOPROPYL ALCOHOL
3SO44Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:35 , TRP A:108 , GLY B:50 , HOH C:326 , HOH C:330binding site for residue IPA A 201
2AC2SOFTWAREGLY A:68 , GLY A:69 , ALA A:70 , GLN A:71binding site for residue SO4 A 202
3AC3SOFTWAREARG B:86 , LYS C:66binding site for residue IPA B 201
4AC4SOFTWAREGLY B:68 , GLY B:69 , ALA B:70 , GLN B:71binding site for residue SO4 B 202
5AC5SOFTWARETYR A:99 , HIS B:62 , TYR B:99 , HIS C:62 , TYR C:99binding site for residue SO4 B 203
6AC6SOFTWAREGLY C:68 , GLY C:69 , ALA C:70 , GLN C:71binding site for residue SO4 C 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Z1T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Z1T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z1T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z1T)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z1T)

(-) 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:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee..hhhhh..hhhhhhhhhhhhhhh.hhhh.eeeee...eeee.......eeeeeee....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeee.hhh.eee..ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 4z1t A   1 xMFIVNTNVPRASVPDGFLSELTQQLAQATGKPPQYIAVHVVPDQLMAFGGSSEPCALCSLHSIGKIGGAQNRSYSKLLCGLLAERLRISPDRVYINYYDMNAANVGWNNSTFA 114
                            |       10        20        30        40        50        60        70        80        90       100       110    
                            |                                                                                                                 
                            1-4N9                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:113
                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhh..hhhhhhhhhhhhhhh.hhhh.eeeee...eeee.......eeeeeee....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeee.hhh.eee..ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 4z1t B   1 xMFIVNTNVPRASVPDGFLSELTQQLAQATGKPPQYIAVHVVPDQLMAFGGSSEPCALCSLHSIGKIGGAQNRSYSKLLCGLLAERLRISPDRVYINYYDMNAANVGWNNSTF 113
                            |       10        20        30        40        50        60        70        80        90       100       110   
                            1-4N9                                                                                                            


Chain C from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee..hhhhh..hhhhhhhhhhhhhhh.hhhh.eeeee...eeee.......eeeeeee....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeee.hhh.eee..ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 4z1t C   1 xMFIVNTNVPRASVPDGFLSELTQQLAQATGKPPQYIAVHVVPDQLMAFGGSSEPCALCSLHSIGKIGGAQNRSYSKLLCGLLAERLRISPDRVYINYYDMNAANVGWNNSTFA 114
                            |       10        20        30        40        50        60        70        80        90       100       110    
                            1-4N9
   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 4Z1T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z1T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z1T)

(-) Gene Ontology  (54, 54)

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
    4N9  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IPA  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4z1t)
 

(-) 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
  4z1t
    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
  MIF_HUMAN | P14174
    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)
  5.3.2.1
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  5.3.3.12
    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
  MIF_HUMAN | P14174
    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
        MIF_HUMAN | P14174: 1ca7 1cgq 1gcz 1gd0 1gif 1ljt 1mif 1p1g 2ooh 2oow 2ooz 3b9s 3ce4 3djh 3dji 3hof 3ijg 3ijj 3jsf 3jsg 3jtu 3l5p 3l5r 3l5s 3l5t 3l5u 3l5v 3smb 3smc 3u18 3wnr 3wns 3wnt 4etg 4eui 4evg 4f2k 4grn 4gro 4grp 4grq 4grr 4gru 4gum 4k9g 4osf 4oyq 4p01 4p0h 4pkk 4pkz 4plu 4trf 4tru 4wr8 4wrb 4xx7 4xx8 4z15 4z1u 5b4o 5bs9 5bsc 5bsi 5bsj 5cg4 5eiz 5hvs 5hvt 5hvv 5j7p 5j7q

(-) Related Entries Specified in the PDB File

4z15 THE SAME PROTEIN COMPLEXED WITH 4-[(4-OXO-2-THIOXO-1,3-THIAZOLAN-3- YL)METHYL]BENZONITRILE
4z1u