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 UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) COMPLEXED WITH BICYCLIC PEPTIDE UK811
 
Authors :  S. Chen, F. Pojer, C. Heinis
Date :  11 Sep 13  (Deposition) - 05 Feb 14  (Release) - 26 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Competitive Inhibitor, Bicyclic Peptide, Inhibitor, Protease, 1, 1', 1''-(1, 3, 5-Triazinane-1, 3, 5-Triyl)Triprop-2-En-1-One (Tata) Cyclization, Extracellular, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Chen, D. Bertoldo, A. Angelini, F. Pojer, C. Heinis
Peptide Ligands Stabilized By Small Molecules.
Angew. Chem. Int. Ed. Engl. V. 53 1602 2014
PubMed-ID: 24453110  |  Reference-DOI: 10.1002/ANIE.201309459

(-) Compounds

Molecule 1 - UROKINASE-TYPE PLASMINOGEN ACTIVATOR CHAIN B
    ChainsA
    EC Number3.4.21.73
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK 293
    Expression System CommonHUMAN
    Expression System PlasmidPSECTAGA
    Expression System Taxid9606
    Expression System Vector TypePLASMID
    FragmentCATALYTIC DOMAIN (UNP RESIDUES 179-423)
    GenePLAU
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymU-PLASMINOGEN ACTIVATOR, UPA
 
Molecule 2 - BICYCLIC PEPTIDE UK811
    ChainsB
    EngineeredYES
    Other DetailsMODIFIED WITH 1,3,5-TRIACRYLOYL-1,3,5-TRIAZINANE (TATA)
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
129N1Ligand/Ion1,1',1''-(1,3,5-TRIAZINANE-1,3,5-TRIYL)TRIPROPAN-1-ONE
2GOL1Ligand/IonGLYCEROL
3NH21Mod. Amino AcidAMINO GROUP
4SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:61 , HIS A:100 , THR A:177 , LYS A:179 , MET A:180 , HOH A:432 , HOH A:461BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWAREPHE A:132 , SER A:164 , HIS A:165 , ARG A:166 , ARG A:206BINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWAREARG A:35 , HIS A:37 , ARG A:37A , HOH A:509 , HOH A:513BINDING SITE FOR RESIDUE GOL A 303
4AC4SOFTWAREGLY A:18 , GLY A:19 , GLU A:20 , PHE A:21 , ASN A:26 , ARG A:35 , VAL A:41 , CYS A:42 , HIS A:57 , CYS A:58 , ASP A:60A , TYR A:60B , TYR A:64 , THR A:97A , LEU A:97B , GLU A:144 , GLN A:145 , ASP A:148 , LYS A:156 , ASP A:189 , SER A:190 , CYS A:191 , GLN A:192 , GLY A:193 , SER A:195 , SER A:214 , TRP A:215 , GLY A:216 , GLY A:218 , GLY A:226 , HOH A:420 , HOH A:430 , HOH A:434 , HOH A:435 , HOH A:466 , HOH B:201 , HOH B:202 , HOH B:203 , HOH B:204 , HOH B:205 , HOH B:206 , HOH B:208 , HOH B:209BINDING SITE FOR BICYCLIC PEPTIDE UK811

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:42 -A:58
2A:50 -A:111
3A:136 -A:201
4A:168 -A:182
5A:191 -A:220

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MNX)

(-) 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:245
                                                                                                                                                                                                                                                                                      
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.hhhhh..eeeeeee.....eeeeeeeeeee..eeeehhhhh....hhh.eeeee............eeeeeeeeee....ee....ee...eeeeee.............................eeeeee...............eeeeeeeehhhhhh....hhhhh...eeeee...............eeeeee..eeeeeeeeee..........eeeee...hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4mnx A   16 IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVENLILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTIALPSMYNDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHT  242
                                    25        35  ||||  41        51       60A||  |   67        77        87        97||     105     ||111       121       131       141       151       161      170A|      179      |187       197       207       217||   | 227       237     
                                                37A|||                     60A||  |                                 97A|          110A|||                                                         170A|            185A|                              218|   |                   
                                                 37B||                      60B|  |                                  97B           110B||                                                          170B             185B                               220   |                   
                                                  37C|                       60C  |                                                 110C|                                                                                                                 223A                   
                                                   37D                          62A                                                  110D                                                                                                                                        

Chain B from PDB  Type:PROTEIN  Length:14
                                               
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author .............. Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                4mnx B    1 LCSDRGCENRWCKx   14
                                    10   |
                                        14-NH2

   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 4MNX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (48, 48)

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
    29N  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NH2  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4mnx)
 

(-) 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
  4mnx
    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
  UROK_HUMAN | P00749
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.21.73
    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
  UROK_HUMAN | P00749
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        UROK_HUMAN | P007491c5w 1c5x 1c5y 1c5z 1ejn 1f5k 1f5l 1f92 1fv9 1gi7 1gi8 1gi9 1gj7 1gj8 1gj9 1gja 1gjb 1gjc 1gjd 1kdu 1lmw 1o3p 1o5a 1o5b 1o5c 1owd 1owe 1owh 1owi 1owj 1owk 1sc8 1sqa 1sqo 1sqt 1u6q 1urk 1vj9 1vja 1w0z 1w10 1w11 1w12 1w13 1w14 2fd6 2i9a 2i9b 2nwn 2o8t 2o8u 2o8w 2r2w 2vin 2vio 2vip 2viq 2viv 2viw 2vnt 3bt1 3bt2 3ig6 3kgp 3khv 3kid 3m61 3mhw 3mwi 3ox7 3oy5 3oy6 3pb1 3qn7 3u73 4dva 4dw2 4fu7 4fu8 4fu9 4fub 4fuc 4fud 4fue 4fuf 4fug 4fuh 4fui 4fuj 4gly 4h42 4jk5 4jk6 4jni 4jnl 4k24 4mnv 4mnw 4mny 4os1 4os2 4os4 4os5 4os6 4os7 4x0w 4x1n 4x1p 4x1q 4x1r 4x1s 4xsk 4zhl 4zhm 4zkn 4zko 4zkr 4zks 5hgg

(-) Related Entries Specified in the PDB File

2nwn CRYSTAL STRUCTURE OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) COMPLEXED WITH MONO-CYCLIC PEPTIDE UPAIN-1
3qn7 CRYSTAL STRUCTURE OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) COMPLEXED WITH BICYCLIC PEPTIDE UK18
4gly CRYSTAL STRUCTURE OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) COMPLEXED WITH BICYCLIC PEPTIDE UK504
4jk5 CRYSTAL STRUCTURE OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) COMPLEXED WITH BICYCLIC PEPTIDE UK18-D-SER
4jk6 CRYSTAL STRUCTURE OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) COMPLEXED WITH BICYCLIC PEPTIDE UK18-D-ABA
4mnv CRYSTAL STRUCTURE OF BICYCLIC PEPTIDE UK729 BOUND AS AN ACYL-ENZYME INTERMEDIATE TO UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA)
4mnw CRYSTAL STRUCTURE OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) COMPLEXED WITH BICYCLIC PEPTIDE UK749
4mny CRYSTAL STRUCTURE OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) COMPLEXED WITH BICYCLIC PEPTIDE UK903