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(-) Description

Title :  CRYSTAL STRUCTURE OF VEGF-A IN COMPLEX WITH VEGFR-1 DOMAINS D1-6
 
Authors :  S. Markovic-Mueller, E. Stuttfeld, M. Asthana, T. Weinert, S. Bliven, K. N. Goldie, K. Kisko, G. Capitani, K. Ballmer-Hofer
Date :  07 Sep 16  (Deposition) - 01 Feb 17  (Release) - 15 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.00
Chains :  Asym./Biol. Unit :  V,W,X,Y
Keywords :  Receptor Tyrosine Kinase, Growth Factor, Immunoglobulin Domain, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Markovic-Mueller, E. Stuttfeld, M. Asthana, T. Weinert, S. Bliven K. N. Goldie, K. Kisko, G. Capitani, K. Ballmer-Hofer
Structure Of The Full-Length Vegfr-1 Extracellular Domain I Complex With Vegf-A.
Structure V. 25 341 2017
PubMed-ID: 28111021  |  Reference-DOI: 10.1016/J.STR.2016.12.012

(-) Compounds

Molecule 1 - VASCULAR ENDOTHELIAL GROWTH FACTOR A
    Chains: V, W
    Engineered: YES
    Expression System: KOMAGATAELLA PASTORIS
    Expression System Plasmid: PPICZALPHA
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Gene: VEGFA, VEGF
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: VEGF-A,VASCULAR PERMEABILITY FACTOR,VPF
 
Molecule 2 - VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1
    Chains: X, Y
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PFASTBAC1
    Expression System Strain: SF21
    Expression System Taxid: 7108
    Expression System Vector Type: PLASMID
    Gene: FLT1, FLT, FRT, VEGFR1
    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

  1234
Asymmetric/Biological Unit : VWXY

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 23)

Asymmetric/Biological Unit (1, 23)
No.NameCountTypeFull Name
1NAG23Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWARENAG X:707binding site for residue NAG X 710
02AC2SOFTWARENAG Y:706binding site for residue NAG Y 711
03AC3SOFTWARETYR V:39 , ASN V:75 , SER V:95 , PHE V:96 , LEU V:97binding site for Mono-Saccharide NAG V 201 bound to ASN V 75
04AC4SOFTWAREGLU W:38 , TYR W:39 , ASN W:75 , SER W:95 , PHE W:96 , LEU W:97binding site for Mono-Saccharide NAG W 201 bound to ASN W 75
05AC5SOFTWAREGLU X:70 , GLN X:98 , ALA X:99 , ASN X:100 , THR X:102 , TYR X:105binding site for Poly-Saccharide residues HIS X 101 through NAG X 702 bound to ASN X 100
06AC6SOFTWAREASN X:196 , THR X:198binding site for Mono-Saccharide NAG X 703 bound to ASN X 196
07AC7SOFTWAREASN X:251binding site for Mono-Saccharide NAG X 704 bound to ASN X 251
08AC8SOFTWARELEU X:308 , ASN X:323binding site for Mono-Saccharide NAG X 705 bound to ASN X 323
09AC9SOFTWAREASP X:372 , GLY X:373 , LEU X:374 , ASN X:402binding site for Mono-Saccharide NAG X 706 bound to ASN X 402
10AD1SOFTWAREASN X:417 , NAG X:710binding site for Mono-Saccharide NAG X 707 bound to ASN X 417
11AD2SOFTWAREASN X:547binding site for Mono-Saccharide NAG X 708 bound to ASN X 547
12AD3SOFTWAREGLY X:570 , MET X:624 , ASN X:625binding site for Mono-Saccharide NAG X 709 bound to ASN X 625
13AD4SOFTWAREGLN Y:98 , ASN Y:100binding site for Mono-Saccharide NAG Y 701 bound to ASN Y 100
14AD5SOFTWAREASN Y:164binding site for Mono-Saccharide NAG Y 702 bound to ASN Y 164
15AD6SOFTWAREARG Y:183 , ASN Y:196 , NAG Y:710binding site for Poly-Saccharide residues NAG Y 703 through NAG Y 704 bound to ASN Y 196
16AD7SOFTWAREASN Y:251 , TYR Y:293binding site for Mono-Saccharide NAG Y 705 bound to ASN Y 251
17AD8SOFTWAREASN Y:323 , NAG Y:711binding site for Mono-Saccharide NAG Y 706 bound to ASN Y 323
18AD9SOFTWAREGLN Y:342 , ASN Y:402 , THR Y:421binding site for Mono-Saccharide NAG Y 707 bound to ASN Y 402
19AE1SOFTWAREASN Y:417binding site for Mono-Saccharide NAG Y 708 bound to ASN Y 417
20AE2SOFTWAREASN Y:547binding site for Mono-Saccharide NAG Y 709 bound to ASN Y 547
21AE3SOFTWAREGLY Y:570 , MET Y:624 , ASN Y:625 , NAG Y:704binding site for Mono-Saccharide NAG Y 710 bound to ASN Y 625

(-) SS Bonds  (18, 18)

Asymmetric/Biological Unit
No.Residues
1V:26 -V:68
2V:51 -W:60
3V:57 -V:102
4V:60 -W:51
5V:61 -V:104
6W:26 -W:68
7W:57 -W:102
8W:61 -W:104
9X:53 -X:107
10X:158 -X:207
11X:252 -X:311
12X:454 -X:535
13X:577 -X:636
14Y:53 -Y:107
15Y:158 -Y:207
16Y:252 -Y:311
17Y:454 -Y:535
18Y:577 -Y:636

(-) Cis Peptide Bonds  (33, 33)

Asymmetric/Biological Unit
No.Residues
1Lys V:48 -Pro V:49
2Lys W:48 -Pro W:49
3Phe X:172 -Pro X:173
4Ser X:235 -Thr X:236
5Gln X:341 -Gln X:342
6Phe X:362 -Pro X:363
7Gly X:373 -Leu X:374
8Pro X:375 -Ala X:376
9Ala X:376 -Thr X:377
10Ile X:459 -Pro X:460
11Asp X:495 -Ser X:496
12Asn X:497 -Met X:498
13Ser X:603 -Ile X:604
14Ile X:604 -Ser X:605
15Met X:609 -Ala X:610
16Glu X:614 -His X:615
17Thr X:643 -Gly X:644
18Gly Y:132 -Arg Y:133
19Phe Y:172 -Pro Y:173
20Ser Y:235 -Thr Y:236
21Gln Y:341 -Gln Y:342
22Phe Y:362 -Pro Y:363
23Gly Y:373 -Leu Y:374
24Pro Y:375 -Ala Y:376
25Ala Y:376 -Thr Y:377
26Pro Y:439 -Asp Y:440
27Ile Y:459 -Pro Y:460
28Asp Y:495 -Ser Y:496
29Asn Y:497 -Met Y:498
30Ser Y:603 -Ile Y:604
31Ile Y:604 -Ser Y:605
32Gln Y:607 -Lys Y:608
33Glu Y:614 -His Y:615

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5T89)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5T89)

(-) Exons   (0, 0)

(no "Exon" information available for 5T89)

(-) 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 V 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.......eeeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 5t89 V  13 EVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPKK 108
                                    22        32        42        52        62        72        82        92       102      


Chain W from PDB  Type:PROTEIN  Length:96
                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhh...eeeeeeeehhhhh......eee..eeeeeeee.......eeeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 5t89 W  13 EVVKFMDVYQRSYCHPIETLVDIFQEYPDEIEYIFKPSCVPLMRCGGCCNDEGLECVPTEESNITMQIMRIKPHQGQHIGEMSFLQHNKCECRPKK 108
                                    22        32        42        52        62        72        82        92       102      


Chain X from PDB  Type:PROTEIN  Length:596
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...............eeeeee....eee..........eeee...eeeeee.........eeeeee...hhhhh.eeeeee.................eeeee.....eee..........eeeee...eee......eeee...eeee...hhhhh.eeeeeeee..eeeeeeeeeee......eeeee....ee......eeeeeeeee.......eeee........eeeeeee.....eeeeeeeee...hhhhheeeeeeee....eeeeeeeee.....eeee.......eeee...eeeeee..eeee...eeee...................eeeeee.hhhhheeeeeeeee....eeeeeeeeeeee...ee.hhh........ee.....ee..eeee.....eeee....................eeeeeeeeeeee..eeeeeeeeeeee....eeeeeeee....eeeeeeeeee.......eeeee........eeeeeee........eeeee........................eeeeeee........eeeeeee.......eee..ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t89 X  32 PELSLKGTQHIMQAGQTLHLQCRGEAAHKWSLPEMVSKESERLSIGKQFCSTLTLNTAQANHTGFYSCKYLAVPTSKTESAIYIFISDTGRPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQTNTIIDVQISTPRPVKLLRGHTLVLNCTATTPLNTRVQMTWSYPDEKNKRASVRRRIDQSHANIFYSVLTIDKMQNKDKGLYTCRVRSGPSFKSVNTSVHIYDKAFITVKHRKQQVLETVAGKRSYRLSMKVKAFPSPEVVWLKDGLPATEKSARYLTRGYSLIIKDVTEEDAGNYTILLSIKQSNVFKNLTATLIVNVKPQIYEKAVSSFPDPALYPLGSRQILTCTAYGIPQPTIKWFWHPCNEESFILDADSNMGNRIESITQRMAIIEGKNKMASTLVVADSRISGIYICIASNKVGTVGRNISFYITDVPNGFHVNLEKMPTEGEDLKLSCTVNKFLYRDVTWILLRTVNNRTMHYSISKQKMAITKEHSITLNLTIMNVSLQDSGTYACRARNVYTGEEILQKKEIT 654
                                    41        51        61        71    ||  89        99       109      |122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282 ||    294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648      
                                                                       76|                            116|                                                                                                                                                                 284|                                                                                                                                                                                      472|                                                                                                                                                                       
                                                                        85                             120                                                                                                                                                                  287                                                                                                                                                                                       487                                                                                                                                                                       


Chain Y from PDB  Type:PROTEIN  Length:597
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee...............eeeeee....eee..........eeee...eeeeee....hhhhheeeeee........eeeeee.................eeeee.....eee..........eeeee....ee......eeee...eeee...hhhhh.eeeeeeee..eeeeeeeeeee......eeeee....ee......eeeeeeeee......eeeee........eeeeeee.....eeeeeeeee........eeeeeeee....eeeeeeeee.....eeee.......eeee...eeeeee..eeee...eeee...................eeeeee.hhhhheeeeeeeee....eeeeeeeeeeee....hhhhh...............eeeeeee.......eee.....................eeeeeeeeeeee..eeeeeeeeeeee....eeeeeeeee..eeeeeeeee.........eeeee........eeeeeee.....eeeeeee.........................eeeeeee.........eeeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t89 Y  31 DPELSLKGTQHIMQAGQTLHLQCRGEAAHKWSLPEMVSKESERLSIGKQFCSTLTLNTAQANHTGFYSCKYLAVPTSTESAIYIFISDTGRPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQTNTIIDVQISTPRPVKLLRGHTLVLNCTATTPLNTRVQMTWSYPDEKNKRASVRRRIDQSHANIFYSVLTIDKMQNKDKGLYTCRVRSGPSFKSVNTSVHIYDKAFITVKHRKQQVLETVAGKRSYRLSMKVKAFPSPEVVWLKDGLPATEKSARYLTRGYSLIIKDVTEEDAGNYTILLSIKQSNVFKNLTATLIVNVKPQIYEKAVSSFPDPALYPLGSRQILTCTAYGIPQPTIKWFWHPCNHEESFILDADSNMGNRIESITQRMAIIEGKNKMASTLVVADSRISGIYICIASNKVGTVGRNISFYITDVPNGFHVNLEKMPTEGEDLKLSCTVNKFLYRDVTWILLRTVNNRTMHYSISKQKMAITKEHSITLNLTIMNVSLQDSGTYACRARNVYTGEEILQKKEIT 654
                                    40        50        60        70     || 88        98       108      |122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282 ||    294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       
                                                                        76|                           115|                                                                                                                                                                 284|                                                                                                                                                                                       473|                                                                                                                                                                       
                                                                         85                            120                                                                                                                                                                  287                                                                                                                                                                                        487
   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 5T89)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5T89)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5T89)

(-) Gene Ontology  (159, 176)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala X:376 - Thr X:377   [ RasMol ]  
    Ala Y:376 - Thr Y:377   [ RasMol ]  
    Asn X:497 - Met X:498   [ RasMol ]  
    Asn Y:497 - Met Y:498   [ RasMol ]  
    Asp X:495 - Ser X:496   [ RasMol ]  
    Asp Y:495 - Ser Y:496   [ RasMol ]  
    Gln X:341 - Gln X:342   [ RasMol ]  
    Gln Y:341 - Gln Y:342   [ RasMol ]  
    Gln Y:607 - Lys Y:608   [ RasMol ]  
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    Glu Y:614 - His Y:615   [ RasMol ]  
    Gly X:373 - Leu X:374   [ RasMol ]  
    Gly Y:132 - Arg Y:133   [ RasMol ]  
    Gly Y:373 - Leu Y:374   [ RasMol ]  
    Ile X:459 - Pro X:460   [ RasMol ]  
    Ile X:604 - Ser X:605   [ RasMol ]  
    Ile Y:459 - Pro Y:460   [ RasMol ]  
    Ile Y:604 - Ser Y:605   [ RasMol ]  
    Lys V:48 - Pro V:49   [ RasMol ]  
    Lys W:48 - Pro W:49   [ RasMol ]  
    Met X:609 - Ala X:610   [ RasMol ]  
    Phe X:172 - Pro X:173   [ RasMol ]  
    Phe X:362 - Pro X:363   [ RasMol ]  
    Phe Y:172 - Pro Y:173   [ RasMol ]  
    Phe Y:362 - Pro Y:363   [ RasMol ]  
    Pro X:375 - Ala X:376   [ RasMol ]  
    Pro Y:375 - Ala Y:376   [ RasMol ]  
    Pro Y:439 - Asp Y:440   [ RasMol ]  
    Ser X:235 - Thr X:236   [ RasMol ]  
    Ser X:603 - Ile X:604   [ RasMol ]  
    Ser Y:235 - Thr Y:236   [ RasMol ]  
    Ser Y:603 - Ile Y:604   [ RasMol ]  
    Thr X:643 - Gly X:644   [ RasMol ]  
 

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  5t89
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  VEGFA_HUMAN | P15692
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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
        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 5fv2 5hhc 5hhd
        VGFR1_HUMAN | P17948: 1flt 1qsv 1qsz 1qty 1rv6 2xac 3hng 4ckv 4cl7 5abd 5ex3

(-) Related Entries Specified in the PDB File

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