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(-) Description

Title :  CRYSTAL STRUCTURE OF VEGFR-1 DOMAIN 2 IN PRESENCE OF CU
 
Authors :  J. -F. Gaucher, M. -B. Lascombe, M. Reille-Seroussi, N. Gagey-Eilstei S. Broussy, P. Coric, B. Seijo, B. Gautier, W. -Q. Liu, F. Huguenot, N. Inguimbert, S. Bouaziz, M. Vidal, I. Broutin
Date :  05 Aug 15  (Deposition) - 28 Sep 16  (Release) - 01 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  E,I,X
Biol. Unit 1:  E  (1x)
Biol. Unit 2:  I  (1x)
Biol. Unit 3:  X  (1x)
Keywords :  Signaling Protein, Vegf, Receptor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. -F. Gaucher, M. Reille-Seroussi, N. Gagey-Eilstein, S. Broussy, P. Coric, B. Seijo, M. -B. Lascombe, B. Gautier, W. -Q. Liu, F. Huguenot N. Inguimbert, S. Bouaziz, M. Vidal, I. Broutin
Biophysical Studies Of The Induced Dimerization Of Human Vegf R Receptor 1 Binding Domain By Divalent Metals Competing With Vegf-A
Plos One V. 11 67755 2016
PubMed-ID: 27942001  |  Reference-DOI: 10.1371/JOURNAL.PONE.0167755

(-) Compounds

Molecule 1 - VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1
    Chains: X, E, I
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA-GAMI PLYSS
    Fragment: DOMAIN-2, RESIDUES 132-226
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: VEGFR-1, FMS-LIKE TYROSINE KINASE 1, FLT-1, TYROSINE-PROTEIN KINASE FRT, TYROSINE-PROTEIN KINASE RECEPTOR FLT, FLT, VASCULAR PERMEABILITY FACTOR RECEPTOR

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : EIX
Biological Unit 1 (1x): E  
Biological Unit 2 (1x):  I 
Biological Unit 3 (1x):   X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1CU5Ligand/IonCOPPER (II) ION
2NA2Ligand/IonSODIUM ION
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2NA-1Ligand/IonSODIUM ION
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2NA-1Ligand/IonSODIUM ION
3SO4-1Ligand/IonSULFATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2NA-1Ligand/IonSODIUM ION
3SO41Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS E:147 , HIS E:223 , HIS X:147 , HIS X:223BINDING SITE FOR RESIDUE CU X1227
2AC2SOFTWAREHIS I:147 , HIS I:223BINDING SITE FOR RESIDUE CU I1225
3AC3SOFTWAREGLY I:132 , ARG I:133 , HIS I:214 , HOH I:2001BINDING SITE FOR RESIDUE CU I1226
4AC4SOFTWAREGLY E:132 , ARG E:133 , HIS X:214 , HOH X:2118BINDING SITE FOR RESIDUE CU X1228
5AC5SOFTWAREHIS E:214 , GLY X:132 , ARG X:133 , HOH X:2001BINDING SITE FOR RESIDUE CU X1229
6AC6SOFTWAREGLU E:137 , PRO E:157 , ARG E:159 , TYR E:220 , HOH E:2004 , HOH E:2021BINDING SITE FOR RESIDUE NA E1227
7AC7SOFTWAREGLU X:137 , TYR X:139 , PRO X:157 , TYR X:220 , HOH X:2010BINDING SITE FOR RESIDUE NA X1230
8AC8SOFTWAREHIS E:223 , ARG E:224 , HOH E:2082BINDING SITE FOR RESIDUE SO4 E1228
9AC9SOFTWAREHIS X:223 , ARG X:224 , HOH X:2048 , HOH X:2119BINDING SITE FOR RESIDUE SO4 X1231

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1E:158 -E:207
2I:158 -I:207
3X:158 -X:207

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Arg E:133 -Pro E:134
2Phe E:172 -Pro E:173
3Arg I:133 -Pro I:134
4Phe I:172 -Pro I:173
5Arg X:133 -Pro X:134
6Phe X:172 -Pro X:173

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ABD)

(-) 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 E from PDB  Type:PROTEIN  Length:95
                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee.....eee..........eeeee...eee......eeee...eeee...hhhhheeeeeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 5abd E 132 GRPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQT 226
                                   141       151       161       171       181       191       201       211       221     


Chain I from PDB  Type:PROTEIN  Length:93
                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeee......eee..........eeeee...ee.......eeee...eeee...hhhhheeeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 5abd I 132 GRPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHR 224
                                   141       151       161       171       181       191       201       211       221   


Chain X from PDB  Type:PROTEIN  Length:95
                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee.....eee..........eeeee...eee......eeee...eeee...hhhhheeeeeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 5abd X 132 GRPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQT 226
                                   141       151       161       171       181       191       201       211       221
   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 5ABD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (54, 54)

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  5abd
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  VGFR1_HUMAN | P17948
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  2.7.10.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        VGFR1_HUMAN | P17948: 1flt 1qsv 1qsz 1qty 1rv6 2xac 3hng 4ckv 4cl7 5ex3 5t89

(-) Related Entries Specified in the PDB File

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