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 THE UROKINASE
 
Authors :  Y. N. Kang, J. A. Stuckey, V. Nienaber, V. Giranda
Date :  28 Jun 12  (Deposition) - 22 Aug 12  (Release) - 22 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.72
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. N. Kang, J. A. Stuckey, V. Nienaber, V. Giranda
Crystal Structure Of The Urokinase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UROKINASE-TYPE PLASMINOGEN ACTIVATOR
    ChainsA
    EC Number3.4.21.73
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GenePLAU
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymU-PLASMINOGEN ACTIVATOR, UPA, UROKINASE-TYPE PLASMINOGEN ACTIVATOR LONG CHAIN A, UROKINASE-TYPE PLASMINOGEN ACTIVATOR SHORT CHAIN A, UROKINASE-TYPE PLASMINOGEN ACTIVATOR CHAIN B

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 15)

Asymmetric/Biological Unit (5, 15)
No.NameCountTypeFull Name
12391Ligand/Ion6-[(Z)-AMINO(IMINO)METHYL]-N-[4-(AMINOMETHYL)PHENYL]-2-NAPHTHAMIDE
2ACT1Ligand/IonACETATE ION
3GOL8Ligand/IonGLYCEROL
4SIN1Ligand/IonSUCCINIC ACID
5SO44Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:46 , ASP A:50 , HIS A:94 , ASP A:192 , SER A:193 , GLN A:195 , SER A:198 , TRP A:218 , GLY A:221 , GLY A:229 , SIN A:302 , HOH A:427BINDING SITE FOR RESIDUE 239 A 301
02AC2SOFTWAREVAL A:30 , CYS A:31 , HIS A:46 , CYS A:47 , GLN A:195 , GLY A:196 , SER A:198 , 239 A:301 , HOH A:706 , HOH A:712BINDING SITE FOR RESIDUE SIN A 302
03AC3SOFTWARELYS A:180 , HIS A:236 , HOH A:494 , HOH A:641 , HOH A:723 , HOH A:751BINDING SITE FOR RESIDUE SO4 A 303
04AC4SOFTWAREARG A:23 , LYS A:53 , HIS A:95 , THR A:178 , LYS A:180 , MET A:181 , HOH A:420 , HOH A:501 , HOH A:709BINDING SITE FOR RESIDUE SO4 A 304
05AC5SOFTWARETYR A:126 , ARG A:233 , HIS A:236 , HOH A:505 , HOH A:506 , HOH A:507BINDING SITE FOR RESIDUE SO4 A 305
06AC6SOFTWAREARG A:21 , ARG A:23 , GLY A:24 , HOH A:765BINDING SITE FOR RESIDUE SO4 A 306
07AC7SOFTWARETHR A:178 , THR A:179 , HOH A:501 , HOH A:502 , HOH A:538 , HOH A:657 , HOH A:709BINDING SITE FOR RESIDUE ACT A 307
08AC8SOFTWARETHR A:28 , TYR A:29 , TYR A:150 , GOL A:311 , HOH A:414 , HOH A:438 , HOH A:580BINDING SITE FOR RESIDUE GOL A 308
09AC9SOFTWAREPRO A:52 , LEU A:81 , ASP A:90 , THR A:91 , GLU A:176 , HOH A:482 , HOH A:492 , HOH A:508BINDING SITE FOR RESIDUE GOL A 309
10BC1SOFTWAREARG A:20 , HIS A:22 , ARG A:23 , TYR A:51 , HOH A:573BINDING SITE FOR RESIDUE GOL A 310
11BC2SOFTWARETHR A:28 , TYR A:29 , ASN A:67 , GOL A:308 , GOL A:314 , HOH A:583 , HOH A:747BINDING SITE FOR RESIDUE GOL A 311
12BC3SOFTWARESER A:37 , PRO A:38 , CYS A:39 , TRP A:40 , LEU A:206 , GLN A:207 , HOH A:512 , HOH A:607 , HOH A:752BINDING SITE FOR RESIDUE GOL A 312
13BC4SOFTWAREGLU A:5 , ASN A:11 , LYS A:142 , MET A:156 , GLN A:195 , HOH A:535 , HOH A:566BINDING SITE FOR RESIDUE GOL A 313
14BC5SOFTWAREVAL A:27 , TYR A:60 , ARG A:63 , ASN A:67 , GOL A:311 , HOH A:651 , HOH A:652BINDING SITE FOR RESIDUE GOL A 314
15BC6SOFTWARELYS A:75 , LYS A:106 , LYS A:225 , HOH A:490 , HOH A:591 , HOH A:594BINDING SITE FOR RESIDUE GOL A 315

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:31 -A:47
2A:39 -A:110
3A:135 -A:204
4A:167 -A:183
5A:194 -A:222

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FUC)

(-) 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:246
                                                                                                                                                                                                                                                                                      
               SCOP domains d4fuca_ A: Urokinase-type plasminogen activator (LMW U-PA), catalytic domain                                                                                                                                                                           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...hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4fuc A   1 IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVENLILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTIALPSMYNDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHTK 246
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240      

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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
    239  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SIN  [ 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 ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4fuc)
 

(-) 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
  4fuc
    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 4fud 4fue 4fuf 4fug 4fuh 4fui 4fuj 4gly 4h42 4jk5 4jk6 4jni 4jnl 4k24 4mnv 4mnw 4mnx 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

4fu7 4fu8 4fu9 4fub 4fud 4fue 4fuf 4fug 4fuh 4fui 4fuj