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(-) Description

Title :  DUAL-ACTING FAB 5A12 IN COMPLEX WITH VEGF
 
Authors :  S. F. Harris, P. Wu
Date :  21 Apr 15  (Deposition) - 01 Jul 15  (Release) - 16 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym./Biol. Unit :  A,B,C,D,H,L
Keywords :  Fab, Daf, Angiogenesis, Tie Receptor, Signaling Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Koenig, C. V. Lee, S. Sanowar, P. Wu, J. Stinson, S. F. Harris, G. Fuh
Deep Sequencing-Guided Design Of A High Affinity Dual Specificity Antibody To Target Two Angiogenic Factors In Neovascular Age-Related Macular Degeneration.
J. Biol. Chem. V. 290 21773 2015
PubMed-ID: 26088137  |  Reference-DOI: 10.1074/JBC.M115.662783

(-) Compounds

Molecule 1 - FRAGMENT ANTIGEN BINDING (FAB) 5A12 HEAVY CHAIN
    Chains: A, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - FRAGMENT ANTIGEN BINDING (FAB) 5A12 LIGHT CHAIN
    Chains: B, L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - VASCULAR ENDOTHELIAL GROWTH FACTOR A
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 217-315
    Gene: VEGFA, VEGF
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: VEGF-A,VASCULAR PERMEABILITY FACTOR,VPF

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDHL

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG C:82 , HIS C:90 , GLY C:92 , GLU C:93 , ARG L:18 , HOH L:410 , HOH L:413binding site for residue SO4 L 301

(-) SS Bonds  (14, 14)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:92
2B:23 -B:88
3C:26 -C:68
4C:51 -D:60
5C:57 -C:102
6C:60 -D:51
7C:61 -C:104
8D:26 -D:68
9D:57 -D:102
10D:61 -D:104
11H:22 -H:92
12H:140 -H:196
13L:23 -L:88
14L:134 -L:194

(-) Cis Peptide Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1Phe A:146 -Pro A:147
2Glu A:148 -Pro A:149
3Ser B:7 -Pro B:8
4Ser B:94 -Pro B:95
5Tyr B:140 -Pro B:141
6Lys C:48 -Pro C:49
7Lys D:48 -Pro D:49
8Phe H:146 -Pro H:147
9Glu H:148 -Pro H:149
10Ser L:7 -Pro L:8
11Ser L:94 -Pro L:95
12Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZFF)

(-) 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:206
                                                                                                                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhheeeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeeee.....eeeee...eeeee........eeeee...eeeeeeeeee.....ee........eee...ee.....eeeeeeeee..hhhhhh.....eehhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4zff A    1 EVQLVESGGGLVQPGGSLRLSCAASGFTISDYWIHWVRQAPGKGLEWVAGITPAGGYTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARFVFFLPYAMDYWGQGTLVTVSSASTKGPSVFPLAPTAALGCLVKDYFPEPVTVSSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDK  209
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||103       113       123  ||   141       151 ||    163       173       183       193       203      
                                                                              52A                            82A||               100A||                       126|               153|                                                     
                                                                                                              82B|                100B|                        135                156                                                     
                                                                                                               82C                 100C                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeeeeeee....eeeeee......eeeee...ee.......eeeeeeeeeeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee......eeee.........eeeeeeeeeehhhhhh...eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4zff B    1 DIQMTQSPSSLSASVGDRVTITCRASQFLSSFGVAWYQQKPGKAPKLLIYGASSLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQGLLSPLTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG  212
                                    10        20       |29        39        49        59        69        79        89        99       109       119       129       139       149  ||   162       172       182       192       202       212
                                                     27A                                                                                                                          152|                                                        
                                                                                                                                                                                   156                                                        


Chain C from PDB  Type:PROTEIN  Length:96
                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhh.eeeeeeeehhhhh......eee..eeeeeeee.......eeeeeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                4zff C   13 EVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPKK  108
                                    22        32        42        52        62        72        82        92       102      


Chain D from PDB  Type:PROTEIN  Length:99
                                                                                                                                    
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh.eeeeeeeehhhhh......eee..eeeeeeee.......eeeeeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                4zff D   11 HHEVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPKKD  109
                                    20        30        40        50        60        70        80        90       100         


Chain H from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhheeeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeeee.....eeeee...eeeee........eeeee...eeeeeeeeee.....eeee.........ee...ee.....eeeeeeeee..hhhhhh.eeeeeehhhhh...eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4zff H    1 EVQLVESGGGLVQPGGSLRLSCAASGFTISDYWIHWVRQAPGKGLEWVAGITPAGGYTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARFVFFLPYAMDYWGQGTLVTVSSASTKGPSVFPLAPTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVE  212
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||103       113       123  ||   141       151       161       171       181       191       201       211 
                                                                              52A                            82A||               100A||                       126|                                                                             
                                                                                                              82B|                100B|                        135                                                                             
                                                                                                               82C                 100C                                                                                                        


Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeeeeeeehhh.eeeeee......eeeee...ee.......eeeeeeeeeeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh...eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4zff L    1 DIQMTQSPSSLSASVGDRVTITCRASQFLSSFGVAWYQQKPGKAPKLLIYGASSLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQGLLSPLTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG  212
                                    10        20       |29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209   
                                                     27A
   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 4ZFF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (122, 122)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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    Lys C:48 - Pro C:49   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        VEGFA_HUMAN | P15692: 1bj1 1cz8 1flt 1kat 1kmx 1mjv 1mkg 1mkk 1qty 1tzh 1tzi 1vgh 1vpf 1vpp 2fjg 2fjh 2qr0 2vgh 2vpf 3bdy 3p9w 3qtk 3s1b 3s1k 3v2a 4deq 4gln 4gls 4kzn 4qaf 4wpb 5dn2 5fv1 5fv2 5hhc 5hhd 5t89

(-) Related Entries Specified in the PDB File

4zfg