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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FGFR2 D2 DOMAIN IN COMPLEX WITH FAB 2B.1.3
 
Authors :  Y. Yin, P. J. Carter
Date :  04 Nov 14  (Deposition) - 16 Sep 15  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.36
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  D,E,F  (1x)
Biol. Unit 2:  A,B,C  (1x)
Keywords :  Fgfr2, Fab, Complex, Antibody, Transferase-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Yin, S. Djakovic, S. Marsters, J. Tien, J. Peng, J. Tremayne, G. Lee, R. M. Neve, Y. Wu, M. Merchant, A. Ashkenazi, P. J. Carter
Redesigning A Monospecific Anti-Fgfr3 Antibody To Add Selectivity For Fgfr2 And Expand Antitumor Activity.
Mol. Cancer Ther. V. 14 2270 2015
PubMed-ID: 26269606  |  Reference-DOI: 10.1158/1535-7163.MCT-14-1050

(-) Compounds

Molecule 1 - FIBROBLAST GROWTH FACTOR RECEPTOR 2
    Chains: F, C
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 153-251
    Gene: FGFR2, BEK, KGFR, KSAM
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: FGFR-2,K-SAM,KGFR,KERATINOCYTE GROWTH FACTOR RECEPTOR
 
Molecule 2 - FAB HEAVY CHAIN
    Chains: B, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - FAB LIGHT CHAIN
    Chains: A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x):    DEF
Biological Unit 2 (1x): ABC   

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4WV1)

(-) Sites  (0, 0)

(no "Site" information available for 4WV1)

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:23 -A:88
2A:134 -A:194
3B:22 -B:92
4B:140 -B:196
5C:176 -C:228
6D:23 -D:88
7D:134 -D:194
8E:22 -E:92
9E:140 -E:196
10F:176 -F:228

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Asn F:181 -Pro F:182
2Glu F:247 -Arg F:248
3Asn C:181 -Pro C:182
4Glu C:247 -Arg C:248
5Phe B:146 -Pro B:147
6Glu B:148 -Pro B:149
7Phe E:146 -Pro E:147
8Glu E:148 -Pro E:149
9Ser A:7 -Pro A:8
10Tyr A:140 -Pro A:141
11Ser D:7 -Pro D:8
12Tyr D:140 -Pro D:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4WV1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WV1)

(-) Exons   (0, 0)

(no "Exon" information available for 4WV1)

(-) 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:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4wv1 A    1 DIQMTQSPSSLSASVGDRVTITCRASQDVDTSLAWYKQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSTGHPQTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    


Chain B from PDB  Type:PROTEIN  Length:224
                                                                                                                                                                                                                                                                 
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee.......eeeeeee.....eeeeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeeeeeeeee......eeeeeee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee........eeeeeeehhhheeeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4wv1 B    1 EVQLVESGGGLVQPGGSLRLSCAASGFTFTSTGISWVRQAPGKGLEWVGRTHLGDGSTNYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARTYGIYDLYVDYTEYVMDYWGQGTLVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC  216
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F||||   106       116       126||     142       152       162       172       182       192       202       212    
                                                                              52A                            82A||               100A|||||100J                        127|                                                                                  
                                                                                                              82B|                100B|||||||                          134                                                                                  
                                                                                                               82C                 100C||||||                                                                                                               
                                                                                                                                    100D|||||                                                                                                               
                                                                                                                                     100E||||                                                                                                               
                                                                                                                                      100F|||                                                                                                               
                                                                                                                                       100G||                                                                                                               
                                                                                                                                        100H|                                                                                                               
                                                                                                                                         100I                                                                                                               


Chain C from PDB  Type:PROTEIN  Length:98
                                                                                                                                   
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...hhhhh.eeeee...eeeee..ee.....eeeeee..ee.hhhhh....eeehhh.eeee...hhhhheeeeeeeee..eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                4wv1 C  151 PYWTNTEKMEKRLHAVPAANTVKFRCPAGGNPMPTMRWLKNGKEFKQEHRIGGYKVRNQHWSLIMESVVPSDKGNYTCVVENEYGSINHTYHLDVVER  248
                                   160       170       180       190       200       210       220       230       240        


Chain D from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4wv1 D    1 DIQMTQSPSSLSASVGDRVTITCRASQDVDTSLAWYKQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSTGHPQTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    


Chain E from PDB  Type:PROTEIN  Length:224
                                                                                                                                                                                                                                                                 
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee.......eeeeeee......eeeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeeeeeeeee......eeeeeee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee........eeeeeeehhhheeeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4wv1 E    1 EVQLVESGGGLVQPGGSLRLSCAASGFTFTSTGISWVRQAPGKGLEWVGRTHLGDGSTNYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARTYGIYDLYVDYTEYVMDYWGQGTLVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC  216
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F||||   106       116       126||     142       152       162       172       182       192       202       212    
                                                                              52A                            82A||               100A|||||100J                        127|                                                                                  
                                                                                                              82B|                100B|||||||                          134                                                                                  
                                                                                                               82C                 100C||||||                                                                                                               
                                                                                                                                    100D|||||                                                                                                               
                                                                                                                                     100E||||                                                                                                               
                                                                                                                                      100F|||                                                                                                               
                                                                                                                                       100G||                                                                                                               
                                                                                                                                        100H|                                                                                                               
                                                                                                                                         100I                                                                                                               


Chain F from PDB  Type:PROTEIN  Length:98
                                                                                                                                   
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...hhhhh.eeeee...eeeee..ee.....eeeeee..ee.hhhhh....eeehhh.eeee...hhhhheeeeeeeee..eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                4wv1 F  151 PYWTNTEKMEKRLHAVPAANTVKFRCPAGGNPMPTMRWLKNGKEFKQEHRIGGYKVRNQHWSLIMESVVPSDKGNYTCVVENEYGSINHTYHLDVVER  248
                                   160       170       180       190       200       210       220       230       240
   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 4WV1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WV1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WV1)

(-) Gene Ontology  (133, 133)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asn C:181 - Pro C:182   [ RasMol ]  
    Asn F:181 - Pro F:182   [ RasMol ]  
    Glu B:148 - Pro B:149   [ RasMol ]  
    Glu C:247 - Arg C:248   [ RasMol ]  
    Glu E:148 - Pro E:149   [ RasMol ]  
    Glu F:247 - Arg F:248   [ RasMol ]  
    Phe B:146 - Pro B:147   [ RasMol ]  
    Phe E:146 - Pro E:147   [ RasMol ]  
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    Tyr A:140 - Pro A:141   [ RasMol ]  
    Tyr D:140 - Pro D:141   [ RasMol ]  
 
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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
        FGFR2_HUMAN | P21802: 1djs 1e0o 1ev2 1gjo 1ii4 1iil 1nun 1oec 1wvz 2fdb 2psq 2pvf 2pvy 2pwl 2py3 2pz5 2pzp 2pzr 2q0b 3b2t 3caf 3cly 3cu1 3dar 3euu 3oj2 3ojm 3ri1 4j23 4j95 4j96 4j97 4j98 4j99 5eg3 5ugl 5ugx 5uhn 5ui0

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4WV1)