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(-) Description

Title :  CRYSTAL STRUCTURE OF FGF RECEPTOR 2 (FGFR2) KINASE DOMAIN HARBORING THE GAIN-OF-FUNCTION K659T MUTATION.
 
Authors :  H. Chen, M. Mohammadi
Date :  15 Feb 13  (Deposition) - 07 Aug 13  (Release) - 28 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  A,B  (1x)
Biol. Unit 6:  C,D  (1x)
Keywords :  Bilobate Protein Kinase Fold, Receptor Tyrosine Kinase, Atp Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Chen, Z. Huang, K. Dutta, S. Blais, T. A. Neubert, X. Li, D. Cowburn, N. J. Traaseth, M. Mohammadi
Cracking The Molecular Origin Of Intrinsic Tyrosine Kinase Activity Through Analysis Of Pathogenic Gain-Of-Function Mutations.
Cell Rep V. 4 376 2013
PubMed-ID: 23871672  |  Reference-DOI: 10.1016/J.CELREP.2013.06.025

(-) Compounds

Molecule 1 - FIBROBLAST GROWTH FACTOR RECEPTOR 2
    ChainsA, B, C, D
    EC Number2.7.10.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)PLYS-S
    Expression System Taxid469008
    FragmentHUMAN FGF RECEPTOR 2 KINASE DOMAIN (UNP RESIDUES 458-768)
    GeneBEK, FGFR2, KGFR, KSAM
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymFGFR-2, K-SAM, KGFR, KERATINOCYTE GROWTH FACTOR RECEPTOR

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D
Biological Unit 5 (1x)AB  
Biological Unit 6 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
1ACP4Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2MG3Ligand/IonMAGNESIUM ION
3SO47Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1ACP1Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1ACP1Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3SO42Ligand/IonSULFATE ION
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
1ACP1Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3SO42Ligand/IonSULFATE ION
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
1ACP1Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3SO41Ligand/IonSULFATE ION
Biological Unit 5 (2, 6)
No.NameCountTypeFull Name
1ACP2Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3SO44Ligand/IonSULFATE ION
Biological Unit 6 (2, 5)
No.NameCountTypeFull Name
1ACP2Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3SO43Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:625 , ARG A:649 , TYR A:657 , THR A:659BINDING SITE FOR RESIDUE SO4 A 801
02AC2SOFTWAREGLY A:488 , GLY A:490 , ALA A:491 , VAL A:495 , ALA A:515 , LYS A:517 , VAL A:564 , GLU A:565 , ALA A:567 , ASP A:626 , ARG A:630 , ASN A:631 , LEU A:633 , ASP A:644 , HOH A:967 , HOH A:968 , HOH A:970 , HOH A:972BINDING SITE FOR RESIDUE ACP A 802
03AC3SOFTWARETHR A:635 , GLU A:636 , ASN A:637 , VAL A:639BINDING SITE FOR RESIDUE SO4 A 803
04AC4SOFTWAREARG B:625 , ARG B:649 , TYR B:657 , THR B:659 , THR B:660 , HOH B:932BINDING SITE FOR RESIDUE SO4 B 801
05AC5SOFTWAREGLY B:488 , GLY B:490 , ALA B:491 , VAL B:495 , ALA B:515 , VAL B:564 , GLU B:565 , ALA B:567 , ASN B:571 , ASP B:626 , ASN B:631 , LEU B:633 , ASP B:644 , HOH B:930 , HOH B:1013BINDING SITE FOR RESIDUE ACP B 802
06AC6SOFTWARETHR A:729 , ASN A:730 , GLU A:731 , ARG B:478 , HOH B:931 , HOH B:992BINDING SITE FOR RESIDUE SO4 B 803
07AC7SOFTWAREARG C:625 , ARG C:649 , TYR C:657 , THR C:659 , THR C:660 , HOH C:922BINDING SITE FOR RESIDUE SO4 C 801
08AC8SOFTWARELEU C:487 , GLY C:488 , PHE C:492 , VAL C:495 , ALA C:515 , LYS C:517 , GLU C:565 , ALA C:567 , ASN C:631 , LEU C:633 , ASP C:644 , MG C:803 , HOH C:959 , HOH C:985BINDING SITE FOR RESIDUE ACP C 802
09AC9SOFTWAREASN C:631 , ASP C:644 , ACP C:802BINDING SITE FOR RESIDUE MG C 803
10BC1SOFTWARETHR C:635 , ASN C:637 , VAL C:639BINDING SITE FOR RESIDUE SO4 C 804
11BC2SOFTWAREARG D:625 , ARG D:649 , TYR D:657 , THR D:659 , HOH D:962BINDING SITE FOR RESIDUE SO4 D 801
12BC3SOFTWAREGLY D:490 , ALA D:491 , PHE D:492 , ALA D:515 , LYS D:517 , VAL D:564 , GLU D:565 , ALA D:567 , ASN D:571 , ARG D:630 , ASN D:631 , LEU D:633 , ASP D:644 , MG D:803 , MG D:804 , HOH D:945 , HOH D:970BINDING SITE FOR RESIDUE ACP D 802
13BC4SOFTWAREASN D:631 , ASP D:644 , ACP D:802BINDING SITE FOR RESIDUE MG D 803
14BC5SOFTWARELYS D:517 , GLU D:534 , ASP D:644 , GLY D:646 , ACP D:802BINDING SITE FOR RESIDUE MG D 804

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4J99)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4J99)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J99)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J99)

(-) Exons   (0, 0)

(no "Exon" information available for 4J99)

(-) 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:280
                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4j99a_ A: Fibroblast growth factor receptor 2                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhh.eeeeeeeee....eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhh........eeeee......eeeee.....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee....ee.....hhhhhhhhhhhhheehhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j99 A 466 YELPEDPKWEFPRDKLTLGKPLGEGAFGQVVMAEAVGIDKDKPKEAVTVAVKMLKDDATEKDLSDLVSEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLRARRPQMTFKDLVSCTYQLARGMEYLASQKCIHRDLAARNVLVTENNVMKIADFGLARDINDYYKTNGRLPVKWMAPEALFDRVYTHQSDVWSFGVLMWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRILTLT 764
                                   475       485       495       505       515       525       535       545       555       565       575     ||600       610       620       630       640       650 ||   |664       674       684       694       704       714       724       734       744       754       764
                                                                                                                                             581|                                                    652| 659|                                                                                                      
                                                                                                                                              597                                                     655  662                                                                                                      

Chain B from PDB  Type:PROTEIN  Length:291
                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4j99b_ B: Fibroblast growth factor receptor 2                                                                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhh.eeeeeeeee....eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee......ee.......hhhhhhhhhhhhheehhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j99 B 467 ELPEDPKWEFPRDKLTLGKPLGEGAFGQVVMAEAVGIDKDKPKEAVTVAVKMLKDDATEKDLSDLVSEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLRARRPPGMEYSYDQMTFKDLVSCTYQLARGMEYLASQKCIHRDLAARNVLVTENNVMKIADFGLARDINNIDYYKTTTNGRLPVKWMAPEALFDRVYTHQSDVWSFGVLMWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRILTLT 764
                                   476       486       496       506       516       526       536       546       556       566       576       586  ||   603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763 
                                                                                                                                                    589|                                                                                                                                                                       
                                                                                                                                                     597                                                                                                                                                                       

Chain C from PDB  Type:PROTEIN  Length:291
                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4j99c_ C: Fibroblast growth factor receptor 2                                                                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhh.eeeeeeeee....eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee......ee.......hhhhhhhhhhhhheehhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j99 C 467 ELPEDPKWEFPRDKLTLGKPLGEGAFGQVVMAEAVGIDKDKPKEAVTVAVKMLKDDATEKDLSDLVSEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLRARRPPGMEYSYDQMTFKDLVSCTYQLARGMEYLASQKCIHRDLAARNVLVTENNVMKIADFGLARDINNIDYYKTTTNGRLPVKWMAPEALFDRVYTHQSDVWSFGVLMWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRILTLT 764
                                   476       486       496       506       516       526       536       546       556       566       576       586  ||   603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763 
                                                                                                                                                    589|                                                                                                                                                                       
                                                                                                                                                     597                                                                                                                                                                       

Chain D from PDB  Type:PROTEIN  Length:281
                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4j99d_ D: Fibroblast growth factor receptor 2                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhh.eeeeeeeee....eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee......ee....hhhhhhhhhhhhheehhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j99 D 465 EYELPEDPKWEFPRDKLTLGKPLGEGAFGQVVMAEAVGIDKDKPKEAVTVAVKMLKDDATEKDLSDLVSEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLRARRQMTFKDLVSCTYQLARGMEYLASQKCIHRDLAARNVLVTENNVMKIADFGLARDINNIDYYKTGRLPVKWMAPEALFDRVYTHQSDVWSFGVLMWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRILTLT 764
                                   474       484       494       504       514       524       534       544       554       564       574     ||600       610       620       630       640       650       663       673       683       693       703       713       723       733       743       753       763 
                                                                                                                                             580|                                                           659|                                                                                                     
                                                                                                                                              597                                                            663                                                                                                     

   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  (1, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J99)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J99)

(-) Gene Ontology  (133, 133)

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 Related Entries

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

UniProtKB/Swiss-Prot
        FGFR2_HUMAN | P218021djs 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 4wv1 5eg3 5ugl 5ugx 5uhn 5ui0

(-) Related Entries Specified in the PDB File

2psq UNPHOSPHORYLATED UNACTIVATED WILD TYPE FGFR2 KINASE DOMAIN
2pvf PHOSPHORYLATED ACTIVATED FGFR2 KINASE DOMAIN
4j95 FGFR2 KINASE DOMAIN HARBORING THE PATHOGENIC K659N MUTATION IN SPACE GROUP C2
4j96 FGFR2 KINASE DOMAIN HARBORING THE PATHOGENIC K659M MUTATION
4j97 FGFR2 KINASE DOMAIN HARBORING THE PATHOGENIC K659E MUTATION
4j98 FGFR2 KINASE DOMAIN HARBORING THE PATHOGENIC K659Q MUTATION