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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE NK1 DOMAIN OF HGF IN COMPLEX WITH ANTI-HGF MONOCLONAL ANTIBODY SFN68.
 
Authors :  Y. J. Kang, K. L. Kim, H. S. Cho, J. H. Chung
Date :  21 Oct 14  (Deposition) - 13 Jan 16  (Release) - 13 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.62
Chains :  Asym./Biol. Unit :  A,H,L
Keywords :  Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. D. Tolbert, J. Daugherty, C. F. Gao, Q. Xie, C. Miranti, E. Gherardi, G. V. Woude, H. E. Xu
A Mechanistic Basis For Converting A Receptor Tyrosine Kinase Agonist To An Antagonist
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HEPATOCYTE GROWTH FACTOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 23-210
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HEPATOPOIETIN-A, SCATTER FACTOR, SF, NK1
 
Molecule 2 - SFN68 FAB
    Chains: H
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Other Details: RABBIT/HUMAN CHIMERIC ANTIBODY
 
Molecule 3 - SFN68 FAB
    Chains: L
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Other Details: RABBIT/HUMAN CHIMERIC ANTIBODY

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : AHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4D3C)

(-) Sites  (0, 0)

(no "Site" information available for 4D3C)

(-) SS Bonds  (9, 9)

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
6H:22 -H:96
7H:143 -H:199
8L:23 -L:88
9L:135 -L:195

(-) Cis Peptide Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1Ile A:156 -Pro A:157
2Phe H:29 -Ser H:30
3Ser H:30 -Thr H:31
4Phe H:149 -Pro H:150
5Glu H:151 -Pro H:152
6Thr L:7 -Pro L:8
7Ser L:94 -Ala L:95
8Tyr L:141 -Pro L:142
9Asp L:152 -Asn L:153

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4D3C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4D3C)

(-) Exons   (0, 0)

(no "Exon" information available for 4D3C)

(-) 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:137
                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee...hhhhhhhhhh.........eee..eee.......eeee.hhh..............................................................eee.......eee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d3c A  37 NTIHEFKKSAKTADQCANRCTRNKGLPFTCKAFVFCLWFPFNSMSDLYENKDYIRNCIIGKGGSYKGTVSITKSGIKCQPWSSMIPHEHSFLPSSYRGKDLQENYCRNPRGEEGGPWCFTSNPEVRYEVCDIPQCSE 208
                                    46 ||     74        84    || 100    || 121       131       141       151       161       171       181       191       201       
                                      48|                    89|      105|                                                                                           
                                       67                     96       117                                                                                           


Chain H from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.......eeeeeee.....eeeeeeee.....eee.......eeeeeehhh.eeeeee...hhhhheeeeeee......ee...eeeee........eeeee....eeeeeeeeeee....eeeee.hhh....eee...ee.....eeeeeeeeee.hhhh....eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4d3c H   1 QQQLVESGGRLVNPGESLTLTCKASGFTFSTYYMSWVRQAPGKGLEWIGYIGTSSGTTYYANSVKGRFTISSDNAQNTVFLQMTSLTDSDTATYFCARGLGRINLWGPGTLVTVSSASTKGPSVFPLAPCSTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVES 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130|      146       156       166       176       186       196       206       216
                                                                                                                                                           130|                                                                               
                                                                                                                                                            137                                                                               


Chain L from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee........eeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeeee.....eee...eeeee.......eeee...hhhhhhh.eeeeeeeeeee.....eeeee.........eeeee.........eeeeeeeeeehhhhhhh...eeeee.......eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d3c L   1 ELDLTQTPSSVSAAVGGTVTINCQASQSVSNLLAWYQQKPGQPPKLLIYGASNLESGVPSRFRGSGSGTEFTLTISGMKAEDAATYYCQSGYYSAGATFGAGTNVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKS 209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   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 4D3C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4D3C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4D3C)

(-) Gene Ontology  (68, 72)

Asymmetric/Biological Unit(hide GO term definitions)

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Asymmetric/Biological Unit
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  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 4d3c)
 
  Sites
(no "Sites" information available for 4d3c)
 
  Cis Peptide Bonds
    Asp L:152 - Asn L:153   [ RasMol ]  
    Glu H:151 - Pro H:152   [ RasMol ]  
    Ile A:156 - Pro A:157   [ RasMol ]  
    Phe H:149 - Pro H:150   [ RasMol ]  
    Phe H:29 - Ser H:30   [ RasMol ]  
    Ser H:30 - Thr H:31   [ RasMol ]  
    Ser L:94 - Ala L:95   [ RasMol ]  
    Thr L:7 - Pro L:8   [ RasMol ]  
    Tyr L:141 - Pro L:142   [ RasMol ]  
 

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  4d3c
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  HGF_HUMAN | P14210
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  IGKC_HUMAN | P01834
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  U3KM01_RABIT | U3KM01
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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 4k3j 4o3t 4o3u 5coe 5cp9 5cs1 5cs3 5cs5 5cs9 5csq 5ct1 5ct2 5ct3
        IGKC_HUMAN | P01834: 1a4j 1a4k 1cly 1d5b 1d5i 1d6v 1dfb 1gaf 1hez 1hkl 1hzh 1i7z 1mim 1n0x 1om3 1op3 1op5 1ucb 2ny7 2o5x 2o5y 2o5z 2qqk 2qql 2qqn 2qsc 2r56 2rfx 2vxq 3b2u 3b2v 3bdy 3be1 3bky 3bn9 3bqu 3c08 3c09 3cfj 3cfk 3csy 3d0l 3d85 3dvg 3dvn 3eyf 3eyo 3eyq 3iu3 3o11 3qct 3qcu 3qcv 3ru8 3u0w 3u7w 3u7y 3vh8 3wuw 3x11 3x12 4d9r 4hix 4nm4 4nm8 4xmp 4xny 4xnz 4xxd 4ydv 5b38 5b39 5c7k 5esv 5esz 5ewi 5veb 5viy

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4D3C)