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(-) Description

Title :  CRYSTAL STRUCTURE OF HVEGF IN COMPLEX WITH VH DOMAIN ANTIBODY
 
Authors :  C. Chung, T. Batuwangala
Date :  02 Feb 16  (Deposition) - 17 Feb 16  (Release) - 23 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.45
Chains :  Asym. Unit :  A,B,C,V,W,X
Biol. Unit 1:  B,C,V,W  (1x)
Biol. Unit 2:  A,X  (2x)
Keywords :  Hormone, Growth Factor Receptor, 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
    Chains: V, W, X
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: VEGF UNP RESIDUES 27-136
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: VEGF-A, VASCULAR PERMEABILITY FACTOR, VPF, VASCULAR ENDOTHELIAL GROWTH FACTOR
 
Molecule 2 - VH DOMAIN ANTIBODY
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: VH DOMAIN ANTIBODY
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCVWX
Biological Unit 1 (1x):  BCVW 
Biological Unit 2 (2x): A    X

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5FV2)

(-) Sites  (0, 0)

(no "Site" information available for 5FV2)

(-) SS Bonds  (14, 14)

Asymmetric Unit
No.Residues
1A:22 -A:96
2B:22 -B:96
3C:22 -C:96
4V:26 -V:68
5V:51 -W:60
6V:57 -V:102
7V:60 -W:51
8V:61 -V:104
9W:26 -W:68
10W:57 -W:102
11W:61 -W:104
12X:26 -X:68
13X:57 -X:102
14X:61 -X:104

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Lys V:48 -Pro V:49
2Lys W:48 -Pro W:49
3Lys X:48 -Pro X:49

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FV2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FV2)

(-) Exons   (0, 0)

(no "Exon" information available for 5FV2)

(-) 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:116
                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee....eeeeeeeee........eeeeee.....eeeeeee......eee........eeeee....eeeeeee..hhhhheeeeee...........eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 5fv2 A   1 EVQLLVSGGGLVQPGGSLRLSCAASGFTFKAYPMMWVRQAPGKGLEWVSEISPSGSYTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDPRKLDYWGQGTLVTVSS 116
                                    10        20        30        40        50        60        70        80        90       100       110      


Chain B from PDB  Type:PROTEIN  Length:115
                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee....eeeeeeeee..hhhhh.eeeeee.....eeeeeee......eee........eeeee....eeeeeee..hhhhheeeeee...........eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 5fv2 B   1 EVQLLVSGGGLVQPGGSLRLSCAASGFTFKAYPMMWVRQAPGKGLEWVSEISPSGSYTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDPRKLDYWGQGTLVTVS 115
                                    10        20        30        40        50        60        70        80        90       100       110     


Chain C from PDB  Type:PROTEIN  Length:116
                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee....eeeeeeeee........eeeeee.....eeeeeee......eee........eeeee....eeeeeee..hhhhheeeeee............eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 5fv2 C   1 EVQLLVSGGGLVQPGGSLRLSCAASGFTFKAYPMMWVRQAPGKGLEWVSEISPSGSYTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDPRKLDYWGQGTLVTVSS 116
                                    10        20        30        40        50        60        70        80        90       100       110      


Chain V from PDB  Type:PROTEIN  Length:96
                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhh..eeeeeeeehhhhh......eee..eeeeeeee.......eeeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 5fv2 V  13 EVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPKK 108
                                    22        32        42        52        62        72        82        92       102      


Chain W from PDB  Type:PROTEIN  Length:97
                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eehhhhhhhhhh.eeeeeeeehhhhh......eee..eeeeeeee.......eeeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 5fv2 W  12 HEVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPKK 108
                                    21        31        41        51        61        71        81        91       101       


Chain X from PDB  Type:PROTEIN  Length:97
                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh.eeeeeeeehhhhh......eee..eeeeeeee.......eeeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 5fv2 X  12 HEVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPKK 108
                                    21        31        41        51        61        71        81        91       101
   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 5FV2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FV2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FV2)

(-) Gene Ontology  (122, 122)

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  Sites
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  Cis Peptide Bonds
    Lys V:48 - Pro V:49   [ RasMol ]  
    Lys W:48 - Pro W:49   [ RasMol ]  
    Lys X:48 - Pro X:49   [ RasMol ]  
 
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  5fv2
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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 5fv1 5hhc 5hhd 5t89

(-) Related Entries Specified in the PDB File

5fv1 CRYSTAL STRUCTURE OF HVEGF IN COMPLEX WITH VK DOMAIN ANTIBODY