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(-) Description

Title :  NGF IN COMPLEX WITH MEDI578 SCFV
 
Authors :  L. -L. Olsson, A. Aagaard
Date :  16 May 16  (Deposition) - 11 Jan 17  (Release) - 11 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.40
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,B,C,D,H,L  (1x)
Biol. Unit 2:  E,F,G,I,J,K  (1x)
Keywords :  Antibody, Complex, Epitope, Ngf, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. L. Dobson, P. W. Devine, J. J. Phillips, D. R. Higazi, C. Lloyd, B. Popovic, J. Arnold, A. Buchanan, A. Lewis, J. Goodman, C. F. Van Der Walle, P. Thornton, L. Vinall, D. Lowne, A. Aagaard, L. L. Olsson, A. Ridderstad Wollberg, F. Welsh, T. K. Karamanos, C. L. Pashley, M. G. Iadanza, N. A. Ranson, A. E. Ashcroft, A. D. Kippen, T. J. Vaughan, S. E. Radford, D. C. Lowe
Engineering The Surface Properties Of A Human Monoclonal Antibody Prevents Self-Association And Rapid Clearance In Vivo.
Sci Rep V. 6 38644 2016
PubMed-ID: 27995962  |  Reference-DOI: 10.1038/SREP38644

(-) Compounds

Molecule 1 - BETA-NERVE GROWTH FACTOR
    Chains: A, B, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET30A
    Expression System Taxid: 469008
    Gene: NGF, NGFB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BETA-NGF
 
Molecule 2 - MEDI578 SCFV, HEAVY CHAIN
    Chains: C, G, H, J
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - MEDI578 SCFV, LIGHT CHAIN
    Chains: D, I, K, L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHIJKL
Biological Unit 1 (1x): ABCD   H   L
Biological Unit 2 (1x):     EFG IJK 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5JZ7)

(-) Sites  (0, 0)

(no "Site" information available for 5JZ7)

(-) SS Bonds  (20, 20)

Asymmetric Unit
No.Residues
1A:15 -A:80
2A:58 -A:108
3A:68 -A:110
4B:15 -B:80
5B:58 -B:108
6B:68 -B:110
7C:22 -C:92
8D:23 -D:88
9E:15 -E:80
10E:58 -E:108
11E:68 -E:110
12F:15 -F:80
13F:58 -F:108
14F:68 -F:110
15G:22 -G:92
16H:22 -H:92
17I:23 -I:88
18J:22 -J:92
19K:23 -K:88
20L:23 -L:88

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5JZ7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JZ7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JZ7)

(-) Exons   (0, 0)

(no "Exon" information available for 5JZ7)

(-) 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 A from PDB  Type:PROTEIN  Length:110
                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee...eeeeee....eee.....eeee..eeee..eeee..eeeeee.................eeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                5jz7 A    7 FHRGEFSVCDSVSVWVGDKTTATDIKGKEVMVLGEVNINNSVFKQYFFETKCRDPNPVDSGCRGIDSKHWNSYCTTTHTFVKALTMDGKQAAWRFIRIDTACVCVLSRKA  116
                                    16        26        36        46        56        66        76        86        96       106       116


Chain B from PDB  Type:PROTEIN  Length:110
                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee...eeeeee....eee.....eeee..eeee..eeee..eeeeee.................eeeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                5jz7 B    7 FHRGEFSVCDSVSVWVGDKTTATDIKGKEVMVLGEVNINNSVFKQYFFETKCRDPNPVDSGCRGIDSKHWNSYCTTTHTFVKALTMDGKQAAWRFIRIDTACVCVLSRKA  116
                                    16        26        36        46        56        66        76        86        96       106       116


Chain C from PDB  Type:PROTEIN  Length:128
                                                                                                                                                                 
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeee.....eeeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeee..eee.............ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                5jz7 C    1 QVQLVQSGAEVKKPGSSVKVSCKASGGTFSTYGISWVRQAPGQGLEWMGGIIPIFDTGNSAQSFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARSSRIYDLNPSLTAYYDMDVWGQGTMVTVSS  113
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|||||  105        
                                                                              52A                            82A||               100A|||||100J|             
                                                                                                              82B|                100B|||||100K             
                                                                                                               82C                 100C||||||               
                                                                                                                                    100D|||||               
                                                                                                                                     100E||||               
                                                                                                                                      100F|||               
                                                                                                                                       100G||               
                                                                                                                                        100H|               
                                                                                                                                         100I               


Chain D from PDB  Type:PROTEIN  Length:110
                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee....hhhhh..eeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeeeee....eeee...eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                5jz7 D    1 QSVLTQPPSVSAAPGQKVTISCSGSSSNIGNNYVSWYQQLPGTAPKLLIYDNNKRPSGIPDRFSGSKSGTSATLGITGLQTGDEADYYCGTWDSSLSAWVFGGGTKLTVL  107
                                    11        21      ||29        39        49        59        69        79        89      ||97       107
                                    9|              27A|                                                                  95A|            
                                    11               27B                                                                   95B            


Chain E from PDB  Type:PROTEIN  Length:110
                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee...eeeeee....eee.....eeee..eee....eee..eeeeee.................eeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                5jz7 E    7 FHRGEFSVCDSVSVWVGDKTTATDIKGKEVMVLGEVNINNSVFKQYFFETKCRDPNPVDSGCRGIDSKHWNSYCTTTHTFVKALTMDGKQAAWRFIRIDTACVCVLSRKA  116
                                    16        26        36        46        56        66        76        86        96       106       116


Chain F from PDB  Type:PROTEIN  Length:110
                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee...eeeeee....eee.....eeee..eeee..eeee..eeeeee.................eeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                5jz7 F    7 FHRGEFSVCDSVSVWVGDKTTATDIKGKEVMVLGEVNINNSVFKQYFFETKCRDPNPVDSGCRGIDSKHWNSYCTTTHTFVKALTMDGKQAAWRFIRIDTACVCVLSRKA  116
                                    16        26        36        46        56        66        76        86        96       106       116


Chain G from PDB  Type:PROTEIN  Length:128
                                                                                                                                                                 
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeee.....eeeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeee..eee.............ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                5jz7 G    1 QVQLVQSGAEVKKPGSSVKVSCKASGGTFSTYGISWVRQAPGQGLEWMGGIIPIFDTGNSAQSFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARSSRIYDLNPSLTAYYDMDVWGQGTMVTVSS  113
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|||||  105        
                                                                              52A                            82A||               100A|||||100J|             
                                                                                                              82B|                100B|||||100K             
                                                                                                               82C                 100C||||||               
                                                                                                                                    100D|||||               
                                                                                                                                     100E||||               
                                                                                                                                      100F|||               
                                                                                                                                       100G||               
                                                                                                                                        100H|               
                                                                                                                                         100I               


Chain H from PDB  Type:PROTEIN  Length:128
                                                                                                                                                                 
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeee.....eeeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeee..eee.............ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                5jz7 H    1 QVQLVQSGAEVKKPGSSVKVSCKASGGTFSTYGISWVRQAPGQGLEWMGGIIPIFDTGNSAQSFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARSSRIYDLNPSLTAYYDMDVWGQGTMVTVSS  113
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|||||  105        
                                                                              52A                            82A||               100A|||||100J|             
                                                                                                              82B|                100B|||||100K             
                                                                                                               82C                 100C||||||               
                                                                                                                                    100D|||||               
                                                                                                                                     100E||||               
                                                                                                                                      100F|||               
                                                                                                                                       100G||               
                                                                                                                                        100H|               
                                                                                                                                         100I               


Chain I from PDB  Type:PROTEIN  Length:110
                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee....hhhhh..eeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeeeee....eeee...eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                5jz7 I    1 QSVLTQPPSVSAAPGQKVTISCSGSSSNIGNNYVSWYQQLPGTAPKLLIYDNNKRPSGIPDRFSGSKSGTSATLGITGLQTGDEADYYCGTWDSSLSAWVFGGGTKLTVL  107
                                    11        21      ||29        39        49        59        69        79        89      ||97       107
                                    9|              27A|                                                                  95A|            
                                    11               27B                                                                   95B            


Chain J from PDB  Type:PROTEIN  Length:128
                                                                                                                                                                 
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeee.....eeeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeee...ee.............ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                5jz7 J    1 QVQLVQSGAEVKKPGSSVKVSCKASGGTFSTYGISWVRQAPGQGLEWMGGIIPIFDTGNSAQSFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARSSRIYDLNPSLTAYYDMDVWGQGTMVTVSS  113
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|||||  105        
                                                                              52A                            82A||               100A|||||100J|             
                                                                                                              82B|                100B|||||100K             
                                                                                                               82C                 100C||||||               
                                                                                                                                    100D|||||               
                                                                                                                                     100E||||               
                                                                                                                                      100F|||               
                                                                                                                                       100G||               
                                                                                                                                        100H|               
                                                                                                                                         100I               


Chain K from PDB  Type:PROTEIN  Length:110
                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee....hhhhh..eeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeeeee....eeee...eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                5jz7 K    1 QSVLTQPPSVSAAPGQKVTISCSGSSSNIGNNYVSWYQQLPGTAPKLLIYDNNKRPSGIPDRFSGSKSGTSATLGITGLQTGDEADYYCGTWDSSLSAWVFGGGTKLTVL  107
                                    11        21      ||29        39        49        59        69        79        89      ||97       107
                                    9|              27A|                                                                  95A|            
                                    11               27B                                                                   95B            


Chain L from PDB  Type:PROTEIN  Length:110
                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee....hhhhh..eeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeeeee....eeee...eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                5jz7 L    1 QSVLTQPPSVSAAPGQKVTISCSGSSSNIGNNYVSWYQQLPGTAPKLLIYDNNKRPSGIPDRFSGSKSGTSATLGITGLQTGDEADYYCGTWDSSLSAWVFGGGTKLTVL  107
                                    11        21      ||29        39        49        59        69        79        89      ||97       107
                                    9|              27A|                                                                  95A|            
                                    11               27B                                                                   95B
   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 5JZ7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JZ7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JZ7)

(-) Gene Ontology  (29, 29)

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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 4edx 4zbn

(-) Related Entries Specified in the PDB File

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