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(-) Description

Title :  NERVE GROWTH FACTOR IN COMPLEX WITH FAB FROM MOUSE MAB 911
 
Authors :  C. Eigenbrot, M. Ultsch
Date :  27 Mar 12  (Deposition) - 02 Apr 14  (Release) - 13 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,H,L,V,W
Keywords :  Cystine Knot, Immunoglobulin, Growth/Survival Factor, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. L. La Porte, C. Eigenbrot, M. Ultsch, W. H. Ho, D. Foletti, A. Forgie K. C. Lindquist, D. L. Shelton, J. Pons
Generation Of A High-Fidelity Antibody Against Nerve Growth Factor Using Library Scanning Mutagenesis And Validation With Structures Of The Initial And Optimized Fab-Antigen Complexes.
Mabs V. 6 1059
PubMed-ID: 24830649

(-) Compounds

Molecule 1 - BETA-NERVE GROWTH FACTOR
    Chains: W, V
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NGF, NGFB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BETA-NGF
 
Molecule 2 - LIGHT CHAIN OF FAB OF MURINE ANTI-NGF
    Chains: A, L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - HEAVY CHAIN OF FAB OF MURINE ANTI-NGF
    Chains: B, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABHLVW

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 4EDX)

(-) SS Bonds  (16, 16)

Asymmetric/Biological Unit
No.Residues
1A:23 -A:88
2A:134 -A:194
3A:214 -B:128
4B:22 -B:92
5B:142 -B:208
6H:22 -H:92
7H:142 -H:208
8L:23 -L:88
9L:134 -L:194
10L:214 -H:128
11V:15 -V:80
12V:58 -V:108
13V:68 -V:110
14W:15 -W:80
15W:58 -W:108
16W:68 -W:110

(-) Cis Peptide Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1Leu A:94 -Pro A:95
2Tyr A:140 -Pro A:141
3Phe B:148 -Pro B:149
4Glu B:150 -Pro B:151
5Trp B:199 -Pro B:200
6Leu L:94 -Pro L:95
7Tyr L:140 -Pro L:141
8Phe H:148 -Pro H:149
9Glu H:150 -Pro H:151
10Trp H:199 -Pro H:200

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EDX)

(-) 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:214
                                                                                                                                                                                                                                                       
               SCOP domains d4edxa1 A:1-107 automated matches                                                                          d4edxa2 A:108-214 automated matches                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4edx A    1 DIQMTQTTSSLSASLGDRVTISCRASQDISNHLNWYQQKPDGTVKLLIYYISRFHSGVPSRFSGSGSGTDYSLTISNLEQEDIATYFCQQSKTLPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    


Chain B from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeee......eeeeee.....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeeeee...eeeeeee...eeeee........eeeee.....eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4edx B    1 QVQLKESGPGLVAPSQSLSITCTVSGFSLIGYDINWVRQPPGKGLEWLGMIWGDGTTDYNSALKSRLSISKDNSKSQVFLKMNSLRTDDTATYSCARGGYYYGTSYYFDYWGQGTTLTVSSASTTPPSVYPLAPVCSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR  228
                                    10        20        30        40        50        60        70        80  |||   87        97   ||||102       112       122     ||139       149    |||164    || 175    || 187       198 ||   |210       220  ||  
                                                                                                            82A||               100A||||                         128|               154|||    169|      180|          196| || 206|            223|  
                                                                                                             82B|                100B|||                          136                156||     171       183           198 ||  208             226  
                                                                                                              82C                 100C||                                              157|                               200|                       
                                                                                                                                   100D|                                               162                                202                       
                                                                                                                                    100E                                                                                                            


Chain H from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeee......eeeeee.....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeeeee...eeeeeee...eeeee........eeeee.....eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4edx H    1 QVQLKESGPGLVAPSQSLSITCTVSGFSLIGYDINWVRQPPGKGLEWLGMIWGDGTTDYNSALKSRLSISKDNSKSQVFLKMNSLRTDDTATYSCARGGYYYGTSYYFDYWGQGTTLTVSSASTTPPSVYPLAPVCSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR  228
                                    10        20        30        40        50        60        70        80  |||   87        97   ||||102       112       122     ||139       149    |||164    || 175    || 187       198 ||   |210       220  ||  
                                                                                                            82A||               100A||||                         128|               154|||    169|      180|          196| || 206|            223|  
                                                                                                             82B|                100B|||                          136                156||     171       183           198 ||  208             226  
                                                                                                              82C                 100C||                                              157|                               200|                       
                                                                                                                                   100D|                                               162                                202                       
                                                                                                                                    100E                                                                                                            


Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains d4edxl1 L:1-107 automated matches                                                                          d4edxl2 L:108-214 automated matches                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4edx L    1 DIQMTQTTSSLSASLGDRVTISCRASQDISNHLNWYQQKPDGTVKLLIYYISRFHSGVPSRFSGSGSGTDYSLTISNLEQEDIATYFCQQSKTLPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    


Chain V from PDB  Type:PROTEIN  Length:101
                                                                                                                                      
               SCOP domains d4edxv_ V: beta-Nerve growth factor                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eeeeee....eee.....eeee..eee....eee..eeeeee............eeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                4edx V   10 GEFSVCDSVSVWVGDKTTATDIKGKEVMVLGEVNINNSVFKQYFFETKCRDGCRGIDSKHWNSYCTTTHTFVKALTMDGKQAAWRFIRIDTACVCVLSRKA  116
                                    19        29        39        49        59||      75        85        95       105       115 
                                                                             60|                                                 
                                                                              67                                                 


Chain W from PDB  Type:PROTEIN  Length:102
                                                                                                                                       
               SCOP domains d4edxw_ W: beta-Nerve growth factor                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee...eeeeee....eee.....eeee..eee....eee..eeeeee.............eeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                4edx W   10 GEFSVCDSVSVWVGDKTTATDIKGKEVMVLGEVNINNSVFKQYFFETKCRDSGCRGIDSKHWNSYCTTTHTFVKALTMDGKQAAWRFIRIDTACVCVLSRKA  116
                                    19        29        39        49        59||      74        84        94       104       114  
                                                                             60|                                                  
                                                                              66
   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  (3, 6)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu B:150 - Pro B:151   [ RasMol ]  
    Glu H:150 - Pro H:151   [ RasMol ]  
    Leu A:94 - Pro A:95   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        NGF_HUMAN | P01138: 1sg1 1www 2ifg 4edw 4zbn 5jz7

(-) Related Entries Specified in the PDB File

4edw