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(-) Description

Title :  NERVE GROWTH FACTOR IN COMPLEX WITH FAB FROM HUMANIZED VERSION OF MOUSE MAB 911 (TANEZUMAB)
 
Authors :  C. Eigenbrot, M. Ultsch
Date :  27 Mar 12  (Deposition) - 02 Apr 14  (Release) - 13 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.48
Chains :  Asym. Unit :  H,L,V
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  V  (2x)
Biol. Unit 3:  H,L,V  (2x)
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: 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 - TANEZUMAB FAB LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - TANEZUMAB FAB HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : HLV
Biological Unit 1 (1x): HL 
Biological Unit 2 (2x):   V
Biological Unit 3 (2x): HLV

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE H:166 , PRO H:167 , VAL H:169 , SER H:177 , LEU H:178 , SER H:179 , GLN L:160 , SER L:176 , THR L:178BINDING SITE FOR RESIDUE GOL H 301

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1H:22 -H:92
2H:140 -H:196
3L:23 -L:88
4L:134 -L:194
5L:214 -H:127
6V:15 -V:80
7V:58 -V:108
8V:68 -V:110

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Ser L:7 -Pro L:8
2Leu L:94 -Pro L:95
3Tyr L:140 -Pro L:141
4Phe H:146 -Pro H:147
5Glu H:148 -Pro H:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EDW)

(-) Sequences/Alignments

Asymmetric 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 H from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeee......eeeeee.....eee...hhh.eeeeeehhh.eeeeee...hhhhheeeeeeeeeee...eeeeeee...eeeee........eeeee.....eeeeeeeeee.....eeee........eee...ee.....eeeeeeeee..........eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4edw H    1 QVQLQESGPGLVKPSETLSLTCTVSGFSLIGYDLNWIRQPPGKGLEWIGIIWGDGTTDYNSAVKSRVTISKDTSKNQFSLKLSSVTAADTAVYYCARGGYWYATSYYFDYWGQGTLVTVSSASTKGPSVFPLAPCSTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSNFGTQTYTCNVDHKPSNTKVDKTVER  213
                                    10        20        30        40        50        60        70        80  |||   87        97   ||||102       112       122     ||138       148       158       168       178       188       198       208     
                                                                                                            82A||               100A||||                         128|                                                                              
                                                                                                             82B|                100B|||                          135                                                                              
                                                                                                              82C                 100C||                                                                                                           
                                                                                                                                   100D|                                                                                                           
                                                                                                                                    100E                                                                                                           


Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains d4edwl1 L:1-107 automated matches                                                                          d4edwl2 L:108-214 automated matches                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4edw L    1 DIQMTQSPSSLSASVGDRVTITCRASQSISNNLNWYQQKPGKAPKLLIYYTSRFHSGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQEHTLPYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  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:106
                                                                                                                                           
               SCOP domains d4edwv_ V: beta-Nerve growth factor                                                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeee....eee.....eeee..eee....eee..eeeeee...............eeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                4edw V    8 HRGEFSVCDSVSVWVGDKTTATDIKGKEVMVLGEVNINNSVFKQYFFETKCRDPNVDGCRGIDSKHWNSYCTTTHTFVKALTMDGKQAAWRFIRIDTACVCVLSRK  115
                                    17        27        37        47        57    ||||69        79        89        99       109      
                                                                                 62|||                                                
                                                                                  64||                                                
                                                                                   65|                                                
                                                                                    67
   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  (3, 3)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (29, 29)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

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        NGF_HUMAN | P01138: 1sg1 1www 2ifg 4edx 4zbn 5jz7

(-) Related Entries Specified in the PDB File

4edx