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(-) Description

Title :  CRYSTAL STRUCTURE OF UPA IN COMPLEX WITH A CAMELID-DERIVED ANTIBODY FRAGMENT
 
Authors :  K. W. Y. Yung, T. Kromann-Hansen, P. A. Andreasen, J. C. K. Ngo
Date :  08 Jan 16  (Deposition) - 01 Jun 16  (Release) - 10 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.97
Chains :  Asym./Biol. Unit :  A,B,S,T
Keywords :  Upa, Nanobody, Serine Protease, Hydrolase-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Kromann-Hansen, E. Oldenburg, K. W. Yung, G. H. Ghassabeh, S. Muyldermans, P. J. Declerck, M. Huang, P. A. Andreasen, J. C. Ngo
A Camelid-Derived Antibody Fragment Targeting The Active Site Of A Serine Protease Balances Between Inhibitor And Substrate Behavior
J. Biol. Chem. V. 291 15156 2016
PubMed-ID: 27226628  |  Reference-DOI: 10.1074/JBC.M116.732503

(-) Compounds

Molecule 1 - UROKINASE-TYPE PLASMINOGEN ACTIVATOR
    ChainsA, B
    EC Number3.4.21.73
    EngineeredYES
    Expression SystemKOMAGATAELLA PASTORIS CBS 7435
    Expression System Taxid981350
    FragmentUNP RESIDUES 179-424
    GenePLAU
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymUPA
 
Molecule 2 - CAMELID DERIVED ANTIBODY FRAGMENT, NB4
    ChainsS, T
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificVICUGNA PACOS
    Organism Taxid30538

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABST

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3SO42Ligand/IonSULFATE ION
4TWN3Ligand/Ion(3S)-3-[(2S,3S,4R)-3,4-DIMETHYLTETRAHYDROFURAN-2-YL]BUTYL LAURATE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:170B , LYS A:223 , ASP A:223A , GLY S:10 , LEU S:11 , GLN S:122 , THR S:124binding site for residue GOL A 301
02AC2SOFTWAREHIS A:170B , LYS A:223 , ASP A:223A , HOH A:404 , GLN T:13binding site for residue GOL A 302
03AC3SOFTWAREHIS B:170B , TYR B:171 , ASP B:223A , HOH B:424 , GOL T:202binding site for residue GOL B 301
04AC4SOFTWARESER B:125 , MET B:126 , ARG B:239binding site for residue SO4 B 302
05AC5SOFTWARETHR B:147 , ARG S:45 , TYR S:95 , TRP S:117 , TWN S:202 , ARG T:45 , TRP T:117 , TWN T:201 , HOH T:341binding site for residue TWN S 201
06AC6SOFTWARETYR A:149 , TYR B:149 , ARG S:45 , HIS S:100 , LEU S:103 , GLU S:115 , TRP S:117 , TWN S:201 , GLU T:44binding site for residue TWN S 202
07AC7SOFTWARESER S:52 , SER S:54 , GLY S:56 , SER S:57 , HOH S:328binding site for residue SO4 S 203
08AC8SOFTWAREMET A:126 , ARG A:239 , HOH A:403 , LEU S:11 , GLN S:13 , SER S:127 , HOH S:317binding site for residue MES S 204
09AC9SOFTWARETYR A:149 , GLU S:44 , TWN S:201 , PHE T:37 , ARG T:45 , LEU T:103 , GLU T:115 , TRP T:117 , HOH T:314 , HOH T:340binding site for residue TWN T 201
10AD1SOFTWAREHIS B:170B , LYS B:223 , ASP B:223A , LYS B:224 , GOL B:301 , GLY T:10 , LEU T:11 , GLN T:122 , THR T:124binding site for residue GOL T 202
11AD2SOFTWARESER T:7 , GLY T:8 , GLY T:9 , THR T:121binding site for residue GOL T 203

(-) SS Bonds  (14, 14)

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
6B:42 -B:58
7B:50 -B:111
8B:136 -B:201
9B:168 -B:182
10B:191 -B:220
11S:22 -S:96
12S:50 -S:104
13T:22 -T:96
14T:50 -T:104

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5HGG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5HGG)

(-) 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 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee.hhhhh..eeeeeee.....eeeeeeeeeee..eeeehhhhh....hhh.eeeee............eeeeeeeeee...............eeeeee.............................eeeeee...............eeeeeeeehhhhhh....hhhhh...eeeee...............eeeee....eeeeeeeee..........eeeee...hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5hgg A   16 IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVENLILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTIALPSMYNDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHTK  243
                                    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|                             217| 223A                    
                                                 37B||                      60B|  |                                  97B           110B||                                                          170B             185B                              219                         
                                                  37C|                       60C  |                                                 110C|                                                                                                                                         
                                                   37D                          62A                                                  110D                                                                                                                                         

Chain B from PDB  Type:PROTEIN  Length:246
                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee.hhhhh..eeeeeee.....eeeeeeeeeee..eeeehhhhh....hhh.eeeee............eeeeeeeeee...............eeeeee.............................eeeeee...............eeeeeeeehhhhhh....hhhhh...eeeee...............eeeee....eeeeeeeee..........eeeee...hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5hgg B   16 IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVENLILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTIALPSMYNDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHTK  243
                                    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|                             217| 223A                    
                                                 37B||                      60B|  |                                  97B           110B||                                                          170B             185B                              219                         
                                                  37C|                       60C  |                                                 110C|                                                                                                                                         
                                                   37D                          62A                                                  110D                                                                                                                                         

Chain S from PDB  Type:PROTEIN  Length:128
                                                                                                                                                                 
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eeee....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeee.................ee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                5hgg S    1 QVQLQESGGGLVQAGGSLRLSCAASGFTLDSYAIGWFRQAPGKEREGVSCISASGGSTNYADSVKGRFTISRDNAKNTVYLQMNSLKSEDTAVYYCAADHPGLCTSESGRRRYLEVWGQGTQVTVSSA  128
                                    10        20        30        40        50        60        70        80        90       100       110       120        

Chain T from PDB  Type:PROTEIN  Length:127
                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eeee....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeee.................ee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                5hgg T    1 QVQLQESGGGLVQAGGSLRLSCAASGFTLDSYAIGWFRQAPGKEREGVSCISASGGSTNYADSVKGRFTISRDNAKNTVYLQMNSLKSEDTAVYYCAADHPGLCTSESGRRRYLEVWGQGTQVTVSS  127
                                    10        20        30        40        50        60        70        80        90       100       110       120       

   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 5HGG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 | 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 4mnx 4mny 4os1 4os2 4os4 4os5 4os6 4os7 4x0w 4x1n 4x1p 4x1q 4x1r 4x1s 4xsk 4zhl 4zhm 4zkn 4zko 4zkr 4zks

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5HGG)