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(-) Description

Title :  CRYSTAL STRUCTURE OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) COMPLEXED WITH BICYCLIC PEPTIDE UK602 (BICYCLIC 1)
 
Authors :  S. Chen, F. Pojer, C. Heinis
Date :  12 Feb 14  (Deposition) - 24 Sep 14  (Release) - 05 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.79
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Bicyclic Peptide, Inhibitor, Protease, Disulfide Bridges, Cyclization, Extracellular, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Chen, R. Gopalakrishnan, T. Schaer, F. Marger, R. Hovius, D. Bertrand, F. Pojer, C. Heinis
Dithiol Amino Acids Can Structurally Shape And Enhance The Ligand-Binding Properties Of Polypeptides.
Nat Chem V. 6 1009 2014
PubMed-ID: 25343607  |  Reference-DOI: 10.1038/NCHEM.2043

(-) Compounds

Molecule 1 - UROKINASE-TYPE PLASMINOGEN ACTIVATOR
    Chains: A
    EC Number: 3.4.21.73
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Common: HUMAN
    Expression System Plasmid: PSECTAGA
    Expression System Strain: HEK293
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN (UNP RESIDUES 179-423)
    Gene: PLAU
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: U-PLASMINOGEN ACTIVATOR, UPA, UROKINASE-TYPE PLASMINOGEN ACTIVATOR LONG CHAIN A, UROKINASE-TYPE PLASMINOGEN ACTIVATOR SHORT CHAIN A, UROKINASE-TYPE PLASMINOGEN ACTIVATOR CHAIN B
 
Molecule 2 - BICYCLIC PEPTIDE UK602 (BICYCLIC 1)
    Chains: B
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
181S1Mod. Amino Acid(4S)-4,5-DISULFANYL-L-NORVALINE
2ACT2Ligand/IonACETATE ION
3NH21Mod. Amino AcidAMINO GROUP
4SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:61 , HIS A:100 , THR A:177 , LYS A:179 , MET A:180 , HOH A:511BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWAREARG A:35 , HIS A:37 , ARG A:37ABINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWARETHR A:23 , SER A:71 , ARG A:72BINDING SITE FOR RESIDUE ACT A 303
4AC4SOFTWAREPHE A:132 , SER A:164 , HIS A:165 , ARG A:166 , ARG A:206BINDING SITE FOR RESIDUE ACT A 304
5AC5SOFTWAREGLU A:20 , PHE A:21 , THR A:23 , ARG A:35 , VAL A:41 , HIS A:57 , CYS A:58 , ASP A:60A , TYR A:60B , TYR A:64 , HIS A:99 , GLN A:154 , SER A:174 , 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:218 , GLY A:226 , HOH A:414 , HOH A:429 , HOH A:449 , HOH A:502 , HOH B:101 , HOH B:102 , HOH B:103 , HOH B:104 , HOH B:105 , HOH B:107 , HOH B:108BINDING SITE FOR CHAIN B OF BICYCLIC PEPTIDE UK602 (BICYCLIC 1)

(-) 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 4OS2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4OS2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OS2)

(-) Exons   (0, 0)

(no "Exon" information available for 4OS2)

(-) 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
                4os2 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
                4os2 B    1 GxLGRGCENHRCLx   14
                             |      10   |
                             2-81S      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 4OS2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OS2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OS2)

(-) Gene Ontology  (48, 48)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        UROK_HUMAN | P00749: 1c5w 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 4mnx 4mny 4os1 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

4gly HUMAN UROKINASE-TYPE PLASMINOGEN ACTIVATOR UPA IN COMPLEX WITH THE TWO-DISULFIDE BRIDGE PEPTIDE UK504
4os1 CRYSTAL STRUCTURE OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) COMPLEXED WITH BICYCLIC PEPTIDE UK601 (BICYCLIC 1)
4os4 CRYSTAL STRUCTURE OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) COMPLEXED WITH BICYCLIC PEPTIDE UK603 (BICYCLIC 1)
4os5 CRYSTAL STRUCTURE OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) COMPLEXED WITH BICYCLIC PEPTIDE UK603 (BICYCLIC 2)
4os6 CRYSTAL STRUCTURE OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) COMPLEXED WITH BICYCLIC PEPTIDE UK604 (BICYCLIC 2)
4os7 CRYSTAL STRUCTURE OF UROKINASE-TYPE PLASMINOGEN ACTIVATOR (UPA) COMPLEXED WITH BICYCLIC PEPTIDE UK607 (BICYCLIC)