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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ENGINEERED LIPOCALIN (ANTICALIN) IN COMPLEX WITH VEGF(8-109)
 
Authors :  T. Giese, A. Skerra
Date :  04 May 14  (Deposition) - 06 May 15  (Release) - 06 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Beta-Barrel, Binding Protein, Engineered Lipocalin, Transport Protein-Signaling Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Giese, A. Skerra
Crystal Structure Of An Anticalin With Specific Blocking Activity Towards Human Vascular Endothelial Growth Factor (Vegf) Reveals Plasticity Of The Lipocalin Fold
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - LIPOCALIN-1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTLC99
    Expression System Strain: JM83
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 23-174
    Gene: ENGINEERED VARIANT, LCN1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TEAR LIPOCALIN, TLC, TEAR PREALBUMIN, TP, VON EBNER GLAND PROTEIN, VEG PROTEIN
 
Molecule 2 - VASCULAR ENDOTHELIAL GROWTH FACTOR A
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PVEGFS
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 34-135
    Gene: VEGFA, VEGF
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: VEGF-A, VASCULAR PERMEABILITY FACTOR, VPF

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2OMA2Ligand/Ion10-{(1R,2R)-2-[(2E)-HEX-2-EN-1-YL]CYCLOPROPYL}DECANOICACID
3SO43Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:22 , LEU A:29 , LEU A:32 , MET A:55 , ILE A:57 , ALA A:66BINDING SITE FOR RESIDUE OMA A 201
2AC2SOFTWAREPRO B:109 , TYR C:45 , SER C:74 , ASN C:75 , ARG C:82 , LYS C:84 , HIS C:90 , HOH C:330BINDING SITE FOR RESIDUE SO4 C 201
3AC3SOFTWARESER A:91 , HIS A:92 , TYR C:25 , GLU C:103 , CYS C:104 , HOH C:305 , HOH C:320 , HOH C:366BINDING SITE FOR RESIDUE SO4 C 202
4AC4SOFTWAREPRO A:109 , GLU C:103 , ARG C:105 , TYR D:45 , ARG D:82 , HIS D:90 , HOH D:303 , HOH D:309BINDING SITE FOR RESIDUE SO4 D 201
5AC5SOFTWAREGLY A:112 , HOH A:327 , ILE D:83 , PRO D:85 , HIS D:86 , GLY D:88 , GLN D:89 , HOH D:306 , HOH D:365BINDING SITE FOR RESIDUE ACT D 202
6AC6SOFTWAREVAL B:13 , MET B:22 , VAL B:24 , VAL B:113 , LEU B:115BINDING SITE FOR RESIDUE OMA B 201

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1A:31 -A:104
2B:31 -B:104
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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys C:48 -Pro C:49
2Lys D:48 -Pro D:49

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QAF)

(-) 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:109
                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeee........eeeeee...eeee.....eeeeeee......eeeeeeee.............eeeee.........eeeee.hhh......eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 4qaf A   8 EEIQDVSGTWYLKAMTVDVGALRCLAGSVIPTTLTTLEGGNLEAKVTMHIKGRSQEVKAVLSKTDEPGIYTAIGGIHVAKIGRSHVKDHYIFYSEGCLSGVPVPGVWLV 116
                                    17        27        37        47        57        67        77        87        97       107         


Chain B from PDB  Type:PROTEIN  Length:89
                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee........eeeeee...eee..eeeee..eeeeee.............eeeee......eeeee.hhh......eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 4qaf B  13 VSGTWYLKAMTVDVGALRCLAGSVIPTTLTTNLEAKVTEVKAVLSKTDEPGIYTAIGGIHVAKIGRSDHYIFYSEGCLSGVPVPGVWLV 116
                                    22        32        42||     |64        74        84      ||97       107         
                                                         43|    54|                          91|                     
                                                          48     63                           95                     


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


Chain D from PDB  Type:PROTEIN  Length:95
                                                                                                                               
               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
                 4qaf D  12 HEVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRP 106
                                    21        31        41        51        61        71        81        91       101
   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  (0, 0)

(no "SCOP Domain" information available for 4QAF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (131, 133)

Asymmetric/Biological Unit(hide GO term definitions)

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    Lys C:48 - Pro C:49   [ RasMol ]  
    Lys D:48 - Pro D:49   [ RasMol ]  
 

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  4qaf
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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
        LCN1_HUMAN | P31025: 1xki 3eyc
        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 4wpb 4zff 5dn2 5fv1 5fv2 5hhc 5hhd 5t89

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4QAF)