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(-) Description

Title :  CRYSTAL STRUCTURE OF HVEGF IN COMPLEX WITH VK DOMAIN ANTIBODY
 
Authors :  C. Chung, A. Walker
Date :  02 Feb 16  (Deposition) - 17 Feb 16  (Release) - 23 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  L,M,V,W
Keywords :  Immune System, Vegf, Domain Antibody, Vascular Endothelial Growth Factor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Walker, C. Chung, M. Neu, M. Burman, T. Batuwangala, G. Jones, C. Tang, M. Steward, M. Mullin, N. Tournier, A. Lewis, J. Korczynska, V. Chung, I. Catchpole
Novel Interaction Mechanism Of A Domain Antibody Based Inhibitor Of Human Vascular Endothelial Growth Factor With Greater Potency Than Ranibizumab And Bevacizumab And Improved Capacity Over Aflibercept.
J. Biol. Chem. V. 291 5500 2016
PubMed-ID: 26728464  |  Reference-DOI: 10.1074/JBC.M115.691162

(-) Compounds

Molecule 1 - VASCULAR ENDOTHELIAL GROWTH FACTOR A
    Chains: V, W
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: VEGF RESIDUES 27-136
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: VEGF-A, VASCULAR PERMEABILITY FACTOR, VPF, VASCULAR ENDOTHE LIAL GROWTH FACTOR
 
Molecule 2 - VK DOMAIN ANTIBODY
    Chains: L, M
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: VK DOMAIN ANTIBODY, RESIDUES 1-108
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : LMVW

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5FV1)

(-) Sites  (0, 0)

(no "Site" information available for 5FV1)

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1L:23 -L:88
2M:23 -M:88
3V:26 -V:68
4V:51 -W:60
5V:57 -V:102
6V:60 -W:51
7V:61 -V:104
8W:26 -W:68
9W:57 -W:102
10W:61 -W:104

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Tyr L:94 -Pro L:95
3Ser M:7 -Pro M:8
4Tyr M:94 -Pro M:95
5Lys V:48 -Pro V:49
6Lys W:48 -Pro W:49

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FV1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FV1)

(-) Exons   (0, 0)

(no "Exon" information available for 5FV1)

(-) 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 L from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeee...eeeeee...hhhhh.eeeeee......ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 5fv1 L   1 DIQMTQSPSSLSASVGDRVTITCRASQWIGPELKWYQQKPGKAPKLLIYHGSILQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYMYYPHTFGQGTKVEIKR 108
                                    10        20        30        40        50        60        70        80        90       100        


Chain M from PDB  Type:PROTEIN  Length:107
                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeee...eeeeee...hhhhh.eeeeee...........eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 5fv1 M   1 DIQMTQSPSSLSASVGDRVTITCRASQWIGPELKWYQQKPGKAPKLLIYHGSILQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYMYYPHTFGQGTKVEIK 107
                                    10        20        30        40        50        60        70        80        90       100       


Chain V from PDB  Type:PROTEIN  Length:95
                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh.eeeeeeeehhhhh......eee..eeeeeeee.......eeeeeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 5fv1 V  14 VVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPKK 108
                                    23        33        43        53        63        73        83        93       103     


Chain W from PDB  Type:PROTEIN  Length:100
                                                                                                                                    
               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
                 5fv1 W  13 EVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPKKDRHH 112
                                    22        32        42        52        62        72        82        92       102       112
   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 5FV1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FV1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FV1)

(-) Gene Ontology  (122, 122)

Asymmetric/Biological Unit(hide GO term definitions)

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  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 5fv1)
 
  Sites
(no "Sites" information available for 5fv1)
 
  Cis Peptide Bonds
    Lys V:48 - Pro V:49   [ RasMol ]  
    Lys W:48 - Pro W:49   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Ser M:7 - Pro M:8   [ RasMol ]  
    Tyr L:94 - Pro L:95   [ RasMol ]  
    Tyr M:94 - Pro M:95   [ RasMol ]  
 

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  5fv1
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  VEGFA_HUMAN | P15692
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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 4zff 5dn2 5fv2 5hhc 5hhd 5t89

(-) Related Entries Specified in the PDB File

5fv2 CRYSTAL STRUCTURE OF HVEGF IN COMPLEX WITH VH DOMAIN ANTIBODY