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(-) Description

Title :  CRYSTAL STRUCTURE OF FGF RECEPTOR 2 (FGFR2) KINASE DOMAIN HARBORING THE PATHOGENIC K659N MUTATION RESPONSIBLE FOR AN UNCLASSIFIED CRANIOSYNOSTOSIS SYNDROME IN SPACE GROUP C2.
 
Authors :  H. Chen, M. Mohammadi
Date :  15 Feb 13  (Deposition) - 07 Aug 13  (Release) - 28 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.38
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 :  Kinase Domain Fold Consisting Of N- And C-Lobes, 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  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1ACP4Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2SO47Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1ACP1Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ACP1Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2SO41Ligand/IonSULFATE ION
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
1ACP1Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2SO43Ligand/IonSULFATE ION
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
1ACP1Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2SO41Ligand/IonSULFATE ION
Biological Unit 5 (2, 5)
No.NameCountTypeFull Name
1ACP2Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2SO43Ligand/IonSULFATE ION
Biological Unit 6 (2, 6)
No.NameCountTypeFull Name
1ACP2Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2SO44Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY 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 , ARG A:630 , ASN A:631 , LEU A:633 , ASP A:644 , HOH A:910BINDING SITE FOR RESIDUE ACP A 801
02AC2SOFTWAREARG A:625 , ARG A:649 , TYR A:657 , THR A:660BINDING SITE FOR RESIDUE SO4 A 802
03AC3SOFTWARETHR A:635 , ASN A:637 , VAL A:639BINDING SITE FOR RESIDUE SO4 A 803
04AC4SOFTWARELEU B:487 , GLU B:489 , GLY B:490 , ALA B:491 , VAL B:495 , ALA B:515 , VAL B:564 , GLU B:565 , ALA B:567 , ASN B:571 , ARG B:630 , ASN B:631 , LEU B:633 , ASP B:644BINDING SITE FOR RESIDUE ACP B 801
05AC5SOFTWAREARG B:625 , ARG B:649 , TYR B:657 , THR B:660BINDING SITE FOR RESIDUE SO4 B 802
06AC6SOFTWAREGLY C:490 , ALA C:491 , VAL C:495 , ALA C:515 , LYS C:517 , GLU C:565 , ALA C:567 , ARG C:630 , LEU C:633 , ASP C:644BINDING SITE FOR RESIDUE ACP C 801
07AC7SOFTWAREARG C:625 , ARG C:649 , TYR C:657 , ASN C:659 , THR C:660BINDING SITE FOR RESIDUE SO4 C 802
08AC8SOFTWARETHR C:635 , GLU C:636 , ASN C:637 , VAL C:639BINDING SITE FOR RESIDUE SO4 C 803
09AC9SOFTWAREARG C:737 , LYS D:724BINDING SITE FOR RESIDUE SO4 C 804
10BC1SOFTWAREGLY 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 , ASN D:631 , LEU D:633 , ASP D:644BINDING SITE FOR RESIDUE ACP D 801
11BC2SOFTWAREARG D:625 , ARG D:649 , ARG D:664BINDING SITE FOR RESIDUE SO4 D 802

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4J95)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4J95)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J95)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J95)

(-) Exons   (0, 0)

(no "Exon" information available for 4J95)

(-) 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:279
                                                                                                                                                                                                                                                                                                                       
               SCOP domains d4j95a_ A: 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...........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j95 A 467 ELPEDPKWEFPRDKLTLGKPLGEGAFGQVVMAEAVGIDKDKPKEAVTVAVKMLKDDATEKDLSDLVSEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLRARRPQMTFKDLVSCTYQLARGMEYLASQKCIHRDLAARNVLVTENNVMKIADFGLARDIYYKNTTNGRLPVKWMAPEALFDRVYTHQSDVWSFGVLMWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRILTLT 764
                                   476       486       496       506       516       526       536       546       556       566       576    || 601       611       621       631       641       651|      665       675       685       695       705       715       725       735       745       755         
                                                                                                                                            581|                                                   651|                                                                                                            
                                                                                                                                             597                                                    656                                                                                                            

Chain B from PDB  Type:PROTEIN  Length:282
                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4j95b_ 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.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4j95 B 468 LPEDPKWEFPRDKLTLGKPLGEGAFGQVVMAEAVGIDKDKPKEAVTVAVKMLKDDATEKDLSDLVSEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLRARRPQMTFKDLVSCTYQLARGMEYLASQKCIHRDLAARNVLVTENNVMKIADFGLARDINNIDYYKNTTNGRLPVKWMAPEALFDRVYTHQSDVWSFGVLMWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRILTLT 764
                                   477       487       497       507       517       527       537       547       557       567       577   ||  602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762  
                                                                                                                                           581|                                                                                                                                                                       
                                                                                                                                            597                                                                                                                                                                       

Chain C from PDB  Type:PROTEIN  Length:281
                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4j95c_ 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......eeee......hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee......ee.......hhhhhhhhhhhhheehhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j95 C 468 LPEDPKWEFPRDKLTLGKPLGEGAFGQVVMAEAVGIDKDKPKEAVTVAVKMLKDDATEKDLSDLVSEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLRARRQMTFKDLVSCTYQLARGMEYLASQKCIHRDLAARNVLVTENNVMKIADFGLARDINNIDYYKNTTNGRLPVKWMAPEALFDRVYTHQSDVWSFGVLMWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRILTLT 764
                                   477       487       497       507       517       527       537       547       557       567       577  ||   603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763 
                                                                                                                                          580|                                                                                                                                                                       
                                                                                                                                           597                                                                                                                                                                       

Chain D from PDB  Type:PROTEIN  Length:271
                                                                                                                                                                                                                                                                                                               
               SCOP domains d4j95d_ 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....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j95 D 467 ELPEDPKWEFPRDKLTLGKPLGEGAFGQVVMAEAVGIDKDKPKEAVTVAVKMLKDDATEKDLSDLVSEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLRARRQMTFKDLVSCTYQLARGMEYLASQKCIHRDLAARNVLVTENNVMKIADFGLARDIGRLPVKWMAPEALFDRVYTHQSDVWSFGVLMWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRILTLT 764
                                   476       486       496       506       516       526       536       546       556       566       576   ||  602       612       622       632       642       663       673       683       693       703       713       723       733       743       753       763 
                                                                                                                                           580|                                                   651|                                                                                                     
                                                                                                                                            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 4J95)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J95)

(-) 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 4j96 4j97 4j98 4j99 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
2pvy FGFR2 KINASE DOMAIN HARBORING THE PATHOGENIC K659N MUTATION IN SPACE GROUP P1
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
4j99 FGFR2 KINASE DOMAIN HARBORING THE PATHOGENIC K659T MUTATION