Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  FGFR1 MUTANT WITH AN INHIBITOR
 
Authors :  T. D. Bunney, S. Wan, N. Thiyagarajan, L. Sutto, S. V. Williams, P. Ashfo H. Koss, M. A. Knowles, F. L. Gervasio, P. V. Coveney, M. Katan
Date :  10 Mar 15  (Deposition) - 18 Mar 15  (Release) - 01 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase, Fgfr, Cancer, Dovitinib, Tki258, Gatekeeper, Gate Keeper (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Bunney, S. Wan, N. Thiyagarajan, L. Sutto, S. V. Williams, P. Ashford, H. Koss, M. A. Knowles, F. L. Gervasio, P. V. Coveney, M. Katan
The Effect Of Mutations On Drug Sensitivity And Kinase Activity Of Fibroblast Growth Factor Receptors: A Combined Experimental And Theoretical Study
Ebiomedicine V. 2 194 2015
PubMed-ID: 26097890  |  Reference-DOI: 10.1016/J.EBIOM.2015.02.009

(-) Compounds

Molecule 1 - FIBROBLAST GROWTH FACTOR RECEPTOR 1
    Chains: A, B
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PJ821
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: C41 LAMBDA 37
    Expression System Vector Type: PLASMID
    Fragment: KINASE DOMAIN, UNP RESIDUES 458-765
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: FGFR-1, BASIC FIBROBLAST GROWTH FACTOR RECEPTOR 1, BFGFR, BFGF-R-1, FMS-LIKE TYROSINE KINASE 2, FLT-2, N-SAM, PROTO-ONCOGENE C-FGR, FIBROBLAST GROWTH FACTOR 1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
138O2Ligand/Ion4-AMINO-5-FLUORO-3-[5-(4-METHYLPIPERAZIN-1-YL)-1H-BENZIMIDAZOL-2-YL]QUINOLIN-2(1H)-ONE
2CL3Ligand/IonCHLORIDE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
138O1Ligand/Ion4-AMINO-5-FLUORO-3-[5-(4-METHYLPIPERAZIN-1-YL)-1H-BENZIMIDAZOL-2-YL]QUINOLIN-2(1H)-ONE
2CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
138O1Ligand/Ion4-AMINO-5-FLUORO-3-[5-(4-METHYLPIPERAZIN-1-YL)-1H-BENZIMIDAZOL-2-YL]QUINOLIN-2(1H)-ONE
2CL-1Ligand/IonCHLORIDE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:492 , ALA A:512 , ILE A:545 , MET A:561 , GLU A:562 , TYR A:563 , ALA A:564 , SER A:565 , LYS A:566 , GLY A:567 , LEU A:630BINDING SITE FOR RESIDUE 38O A1000
2AC2SOFTWARELEU B:484 , ALA B:512 , ILE B:545 , MET B:561 , GLU B:562 , TYR B:563 , ALA B:564 , SER B:565 , GLY B:567 , LEU B:630BINDING SITE FOR RESIDUE 38O B1000
3AC3SOFTWAREARG A:570 , ARG A:627 , ARG A:661BINDING SITE FOR RESIDUE CL A1765
4AC4SOFTWARELYS A:618BINDING SITE FOR RESIDUE CL A1766
5AC5SOFTWAREARG B:570 , ARG B:627 , ARG B:661BINDING SITE FOR RESIDUE CL B1763

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AM7)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Val A:460 -Ser A:461
2Asn B:659 -Gly B:660

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AM7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AM7)

(-) Exons   (0, 0)

(no "Exon" information available for 5AM7)

(-) 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:294
                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ................hhh.eeeeeeee..eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee.......hhhhh..........hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5am7 A 458 AGVSEYELPEDPRWELPRDRLVLGKPLGEGQVVLAEAIGLDKDKPNRVTKVAVKMLKSDATEKDLSDLISEMEMMKMIGKHKNIINLLGACTQDGPLYVIMEYASKGNLREYLQARRPPGPEEQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDNVMKIADFGLARDIHHIDYYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFTLGGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRIVALTSNQ 764
                                   467       477       490       500       510       520       530       540       550       560       570       580|      600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760    
                                                      486|                                                                                       580|                                                                                                                                                                             
                                                       490                                                                                        591                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:287
                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhh.eeeeeeee..eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee.................hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5am7 B 458 AGVSEYELPEDPRWELPRDRLVLGKPLGEGQVVLAEAIGLDKDKPNRVTKVAVKMLKSDATEKDLSDLISEMEMMKMIGKHKNIINLLGACTQDGPLYVIMEYASKGNLREYLQARRPPGPEEQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDNVMKIADFGLARDYYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFTLGGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRIVALTS 762
                                   467       477       490       500       510       520       530       540       550       560       570       580|      600       610       620       630       640      |655       665       675       685       695       705       715       725       735       745       755       
                                                      486|                                                                                       580|                                                     647|                                                                                                             
                                                       490                                                                                        591                                                      653
   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 5AM7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AM7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AM7)

(-) Gene Ontology  (98, 98)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    38O  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asn B:659 - Gly B:660   [ RasMol ]  
    Val A:460 - Ser A:461   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5am7
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  FGFR1_HUMAN | P11362
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.10.1
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  FGFR1_HUMAN | P11362
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        FGFR1_HUMAN | P11362: 1agw 1cvs 1evt 1fgi 1fgk 1fq9 1xr0 2cr3 2fgi 3c4f 3dpk 3gqi 3gql 3js2 3krj 3krl 3kxx 3ky2 3ojv 3rhx 3tt0 4f63 4f64 4f65 4nk9 4nka 4nks 4rwi 4rwj 4rwk 4rwl 4uwb 4uwc 4uwy 4v01 4v04 4v05 4wun 4zsa 5a46 5a4c 5am6 5b7v 5ew8 5flf 5uq0 5ur1 5vnd

(-) Related Entries Specified in the PDB File

5am6 NATIVE FGFR1 WITH AN INHIBITOR