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(-) Description

Title :  THE STRUCTURE OF THE NK1 FRAGMENT OF HGF/SF COMPLEXED WITH MES
 
Authors :  A. G. Sigurdardottir, A. Winter, A. Sobkowicz, M. Fragai, D. Y. Chirgad D. B. Ascher, T. L. Blundell, E. Gherardi
Date :  23 Jul 15  (Deposition) - 12 Aug 15  (Release) - 26 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hgf/Sf, Nk1 Fragment, Fragment Based Drug Discovery, Growth Factor, Cell Cycle, Hormone, New Chemical Entity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. G. Sigurdardottir, A. Winter, A. Sobkowicz, M. Fragai, D. Y. Chirgadze, D. B. Ascher, T. L. Blundell, E. Gherardi
Exploring The Chemical Space Of The Lysine-Binding Pocket O The First Kringle Domain Of Hepatocyte Growth Factor/Scatte Factor (Hgf/Sf) Yields A New Class Of Inhibitors Of Hgf/Sf-Met Binding
Chem Sci V. 6 6147 2015
PubMed: search  |  Reference-DOI: 10.1039/C5SC02155C

(-) Compounds

Molecule 1 - HEPATOCYTE GROWTH FACTOR
    Chains: A, B
    Engineered: YES
    Expression System: KOMAGATAELLA PASTORIS CBS 7435
    Expression System Taxid: 981350
    Fragment: UNP RESIDUES 28-210
    Gene: HGF, HPTA
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HEPATOPOIETIN-A,SCATTER FACTOR,SF

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE B:162 , TRP B:188 , PHE B:190 , ARG B:197 , TYR B:198 , EDO B:302 , HOH B:434 , HOH B:457binding site for residue MES B 301
2AC2SOFTWAREGLU B:183 , GLY B:185 , GLY B:186 , VAL B:200 , MES B:301binding site for residue EDO B 302

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1A:70 -A:96
2A:74 -A:84
3A:128 -A:206
4A:149 -A:189
5A:177 -A:201
6B:70 -B:96
7B:74 -B:84
8B:128 -B:206
9B:149 -B:189
10B:177 -B:201

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ile A:156 -Pro A:157
2Ile B:156 -Pro B:157

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CS9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CS9)

(-) Exons   (0, 0)

(no "Exon" information available for 5CS9)

(-) 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    
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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:172
                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhh.eeeeeeeeeee.......eeee..hhhhhhhhhhhh........eeeee....eeeee........eeeeeeeeeeeeee.hhh.....................................hhhhhh...................eee.......eee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cs9 A  38 TIHEFKKSAKTTLIKIDPALKIKTKKVNTADQCANRCTRNKGLPFTCKAFVFDKARKQCLWFPFNSMSSGVKKEFGHEFDLYENKDYIRNCIIGKGRSYKGTVSITKSGIKCQPWSSMIPHEHSFLPSSYRGKDLQENYCRNPRGEEGGPWCFTSNPEVRYEVCDIPQCSEV 209
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207  


Chain B from PDB  Type:PROTEIN  Length:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhh.eeeeeeeeeee.......eeee..hhhhhhhhhhhh........eeeee....eeeee........eeeeeeeeeeeeee.hhh.....................................hhhhh....................eee.......eee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5cs9 B  36 RNTIHEFKKSAKTTLIKIDPALKIKTKKVNTADQCANRCTRNKGLPFTCKAFVFDKARKQCLWFPFNSMSSGVKKEFGHEFDLYENKDYIRNCIIGKGRSYKGTVSITKSGIKCQPWSSMIPHEHSFLPSSYRGKDLQENYCRNPRGEEGGPWCFTSNPEVRYEVCDIPQCSEV 209
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205
   Legend:   → Mismatch (orange background)
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  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 5CS9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CS9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CS9)

(-) Gene Ontology  (47, 47)

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
        HGF_HUMAN | P14210: 1bht 1gmn 1gmo 1gp9 1nk1 1shy 1si5 2ced 2cee 2ceg 2hgf 2qj2 3hms 3hmt 3hn4 3mkp 3sp8 4d3c 4k3j 4o3t 4o3u 5coe 5cp9 5cs1 5cs3 5cs5 5csq 5ct1 5ct2 5ct3

(-) Related Entries Specified in the PDB File

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