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(-) Description

Title :  STRUCTURE OF FIBROBLAST GROWTH FACTOR 9
 
Authors :  H. J. Hecht, R. Adar, B. Hofmann, O. Bogin, H. Weich, A. Yayon
Date :  16 Nov 00  (Deposition) - 07 Mar 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Biol. Unit 3:  A (1x),B (1x),C (1x),D (1x)
Biol. Unit 4:  A,B,C,D  (1x)
Keywords :  Fibroblast Growth Factor, Hormone-Growth Factor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. J. Hecht, R. Adar, B. Hofmann, O. Bogin, H. Weich, A. Yayon
Structure Of Fibroblast Growth Factor 9 Shows A Symmetric Dimer With Unique Receptor- And Heparin-Binding Interfaces.
Acta Crystallogr. , Sect. D V. 57 378 2001
PubMed-ID: 11223514  |  Reference-DOI: 10.1107/S0907444900020813

(-) Compounds

Molecule 1 - FIBROBLAST GROWTH FACTOR 9
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemUNIDENTIFIED BACULOVIRUS
    Expression System Cell LineSF9
    Expression System PlasmidPBACPAK9
    Expression System Taxid10469
    Expression System Vector TypeVIRUS
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A  D
Biological Unit 2 (1x) BC 
Biological Unit 3 (1x)A (1x)B (1x)C (1x)D (1x)
Biological Unit 4 (1x)ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 22)

Asymmetric Unit (3, 22)
No.NameCountTypeFull Name
1FUC3Ligand/IonALPHA-L-FUCOSE
2NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SO412Ligand/IonSULFATE ION
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1FUC2Ligand/IonALPHA-L-FUCOSE
2NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SO46Ligand/IonSULFATE ION
Biological Unit 2 (3, 10)
No.NameCountTypeFull Name
1FUC1Ligand/IonALPHA-L-FUCOSE
2NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SO46Ligand/IonSULFATE ION
Biological Unit 3 (3, 12)
No.NameCountTypeFull Name
1FUC2Ligand/IonALPHA-L-FUCOSE
2NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SO46Ligand/IonSULFATE ION
Biological Unit 4 (3, 22)
No.NameCountTypeFull Name
1FUC3Ligand/IonALPHA-L-FUCOSE
2NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SO412Ligand/IonSULFATE ION

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:79 , NAG A:652 , FUC A:653 , HOH A:708BINDING SITE FOR RESIDUE NAG A 651
02AC2SOFTWARENAG A:651BINDING SITE FOR RESIDUE NAG A 652
03AC3SOFTWAREPRO A:78 , PHE A:92 , NAG A:651 , FUC C:653BINDING SITE FOR RESIDUE FUC A 653
04AC4SOFTWAREASN B:79BINDING SITE FOR RESIDUE NAG B 651
05AC5SOFTWAREPHE C:77 , ASN C:79 , NAG C:652 , FUC C:653BINDING SITE FOR RESIDUE NAG C 651
06AC6SOFTWARENAG C:651 , FUC C:653BINDING SITE FOR RESIDUE NAG C 652
07AC7SOFTWAREFUC A:653 , PHE C:92 , NAG C:651 , NAG C:652BINDING SITE FOR RESIDUE FUC C 653
08AC8SOFTWARETHR A:158 , GLY A:159 , PHE D:77 , ASN D:79 , THR D:81 , NAG D:652 , FUC D:653 , HOH D:701BINDING SITE FOR RESIDUE NAG D 651
09AC9SOFTWAREPHE D:77 , NAG D:651 , FUC D:653BINDING SITE FOR RESIDUE NAG D 652
10BC1SOFTWAREPHE D:92 , NAG D:651 , NAG D:652 , HOH D:662BINDING SITE FOR RESIDUE FUC D 653
11BC2SOFTWAREARG A:160 , ARG A:161 , TYR A:163 , ARG A:180BINDING SITE FOR RESIDUE SO4 A 290
12BC3SOFTWAREGLY B:159 , ARG B:160 , ARG B:161 , TYR B:163 , ARG B:180BINDING SITE FOR RESIDUE SO4 B 291
13BC4SOFTWAREARG C:160 , ARG C:161 , TYR C:163 , ARG C:180 , HOH C:674BINDING SITE FOR RESIDUE SO4 C 292
14BC5SOFTWAREARG D:160 , ARG D:161 , TYR D:163 , ARG D:180 , HOH D:660 , HOH D:700BINDING SITE FOR RESIDUE SO4 D 293
15BC6SOFTWAREARG A:137 , LYS A:154 , ARG A:161BINDING SITE FOR RESIDUE SO4 A 294
16BC7SOFTWAREARG B:137 , LYS B:154 , ARG B:161BINDING SITE FOR RESIDUE SO4 B 295
17BC8SOFTWAREARG C:137 , LYS C:154 , ARG C:161BINDING SITE FOR RESIDUE SO4 C 296
18BC9SOFTWAREARG D:137 , LYS D:154 , ARG D:161 , HOH D:673BINDING SITE FOR RESIDUE SO4 D 297
19CC1SOFTWAREARG C:160 , LYS C:179BINDING SITE FOR RESIDUE SO4 C 298
20CC2SOFTWAREARG A:173 , ARG A:177BINDING SITE FOR RESIDUE SO4 A 299
21CC3SOFTWAREARG D:173 , ARG D:177BINDING SITE FOR RESIDUE SO4 D 300
22CC4SOFTWAREARG C:173 , ARG C:177BINDING SITE FOR RESIDUE SO4 C 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1G82)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1G82)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 8)

Asymmetric Unit (2, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020944I94VFGF9_HUMANPolymorphism12427696A/B/C/DI94V
2UniProtVAR_063254S99NFGF9_HUMANDisease (SYNS3)121918322A/B/C/DS99N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020944I94VFGF9_HUMANPolymorphism12427696A/DI94V
2UniProtVAR_063254S99NFGF9_HUMANDisease (SYNS3)121918322A/DS99N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020944I94VFGF9_HUMANPolymorphism12427696B/CI94V
2UniProtVAR_063254S99NFGF9_HUMANDisease (SYNS3)121918322B/CS99N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (2, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020944I94VFGF9_HUMANPolymorphism12427696A/B/C/DI94V
2UniProtVAR_063254S99NFGF9_HUMANDisease (SYNS3)121918322A/B/C/DS99N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 4 (2, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020944I94VFGF9_HUMANPolymorphism12427696A/B/C/DI94V
2UniProtVAR_063254S99NFGF9_HUMANDisease (SYNS3)121918322A/B/C/DS99N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HBGF_FGFPS00247 HBGF/FGF family signature.FGF9_HUMAN122-145
 
 
 
  4A:122-145
B:122-145
C:122-145
D:122-145
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HBGF_FGFPS00247 HBGF/FGF family signature.FGF9_HUMAN122-145
 
 
 
  2A:122-145
-
-
D:122-145
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HBGF_FGFPS00247 HBGF/FGF family signature.FGF9_HUMAN122-145
 
 
 
  2-
B:122-145
C:122-145
-
Biological Unit 3 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HBGF_FGFPS00247 HBGF/FGF family signature.FGF9_HUMAN122-145
 
 
 
  4A:122-145
B:122-145
C:122-145
D:122-145
Biological Unit 4 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HBGF_FGFPS00247 HBGF/FGF family signature.FGF9_HUMAN122-145
 
 
 
  4A:122-145
B:122-145
C:122-145
D:122-145

(-) Exons   (3, 12)

Asymmetric Unit (3, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003823531ENSE00001491832chr13:22245522-22246328807FGF9_HUMAN1-93934A:52-93
B:51-93
C:52-93
D:49-93
42
43
42
45
1.3aENST000003823533aENSE00000678905chr13:22255181-22255284104FGF9_HUMAN93-127354A:93-127
B:93-127
C:93-127
D:93-127
35
35
35
35
1.4cENST000003823534cENSE00001491824chr13:22275329-222786373309FGF9_HUMAN128-208814A:128-208
B:128-207
C:128-206
D:128-203
81
80
79
76

(-) 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:157
 aligned with FGF9_HUMAN | P31371 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:157
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       
           FGF9_HUMAN    52 TDLDHLKGILRRRQLYCRTGFHLEIFPNGTIQGTRKDHSRFGILEFISIAVGLVSIRGVDSGLYLGMNEKGELYGSEKLTQECVFREQFEENWYNTYSSNLYKHVDTGRRYYVALNKDGTPREGTRTKRHQKFTHFLPRPVDPDKVPELYKDILSQS 208
               SCOP domains d1g82a_ A: Fibroblast growth factor 9, FGF9                                                                                                                   SCOP domains
               CATH domains 1g82A00 A:52-208  [code=2.80.10.50, no name defined]                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh.eeeeee....eeee.....eeee.........eeeeeee..eeeeee.....eeee.....eeee...hhhh.eeeeeee..eeeeeeeeee......eee..................hhhh.eeee..hhhhh.hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------V----N------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------HBGF_FGF  PDB: A:122-145--------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:52-93 UniProt: 1-93      ----------------------------------Exon 1.4c  PDB: A:128-208 UniProt: 128-208                                        Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------Exon 1.3a  PDB: A:93-127           --------------------------------------------------------------------------------- Transcript 1 (2)
                 1g82 A  52 TDLDHLKGILRRRQLYCRTGFHLEIFPNGTIQGTRKDHSRFGILEFISIAVGLVSIRGVDSGLYLGMNEKGELYGSEKLTQECVFREQFEENWYNTYSSNLYKHVDTGRRYYVALNKDGTPREGTRTKRHQKFTHFLPRPVDPDKVPELYKDILSQS 208
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       

Chain B from PDB  Type:PROTEIN  Length:157
 aligned with FGF9_HUMAN | P31371 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:157
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       
           FGF9_HUMAN    51 VTDLDHLKGILRRRQLYCRTGFHLEIFPNGTIQGTRKDHSRFGILEFISIAVGLVSIRGVDSGLYLGMNEKGELYGSEKLTQECVFREQFEENWYNTYSSNLYKHVDTGRRYYVALNKDGTPREGTRTKRHQKFTHFLPRPVDPDKVPELYKDILSQ 207
               SCOP domains d1g82b_ B: Fibroblast growth factor 9, FGF9                                                                                                                   SCOP domains
               CATH domains 1g82B00 B:51-207  [code=2.80.10.50, no name defined]                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh.eeeeee...eeeee.....eeee....hhhh.eeeeeee..eeeeee.....eeee.....eeee...hhhh.eeeeeee..eeeeeeeeee......eee..........hhhhh...hhhh.eeee.........hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------V----N------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------HBGF_FGF  PDB: B:122-145-------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:51-93 UniProt: 1-93       ----------------------------------Exon 1.4c  PDB: B:128-207 UniProt: 128-208 [INCOMPLETE]                          Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------Exon 1.3a  PDB: B:93-127           -------------------------------------------------------------------------------- Transcript 1 (2)
                 1g82 B  51 VTDLDHLKGILRRRQLYCRTGFHLEIFPNGTIQGTRKDHSRFGILEFISIAVGLVSIRGVDSGLYLGMNEKGELYGSEKLTQECVFREQFEENWYNTYSSNLYKHVDTGRRYYVALNKDGTPREGTRTKRHQKFTHFLPRPVDPDKVPELYKDILSQ 207
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       

Chain C from PDB  Type:PROTEIN  Length:155
 aligned with FGF9_HUMAN | P31371 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:155
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201     
           FGF9_HUMAN    52 TDLDHLKGILRRRQLYCRTGFHLEIFPNGTIQGTRKDHSRFGILEFISIAVGLVSIRGVDSGLYLGMNEKGELYGSEKLTQECVFREQFEENWYNTYSSNLYKHVDTGRRYYVALNKDGTPREGTRTKRHQKFTHFLPRPVDPDKVPELYKDILS 206
               SCOP domains d1g82c_ C: Fibroblast growth factor 9, FGF9                                                                                                                 SCOP domains
               CATH domains 1g82C00 C:52-206  [code=2.80.10.50, no name defined]                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhheeeeee...eeeee.....eeee....hhhh.eeeeeee..eeeeee.....eeee.....eeee...hhhh.eeeee.....eeeeeeeee......eee..........hhhhh...hhhh.eeee..hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------V----N----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------HBGF_FGF  PDB: C:122-145------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: C:52-93 UniProt: 1-93      ----------------------------------Exon 1.4c  PDB: C:128-206 UniProt: 128-208 [INCOMPLETE]                         Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------Exon 1.3a  PDB: C:93-127           ------------------------------------------------------------------------------- Transcript 1 (2)
                 1g82 C  52 TDLDHLKGILRRRQLYCRTGFHLEIFPNGTIQGTRKDHSRFGILEFISIAVGLVSIRGVDSGLYLGMNEKGELYGSEKLTQECVFREQFEENWYNTYSSNLYKHVDTGRRYYVALNKDGTPREGTRTKRHQKFTHFLPRPVDPDKVPELYKDILS 206
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201     

Chain D from PDB  Type:PROTEIN  Length:155
 aligned with FGF9_HUMAN | P31371 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:155
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198     
           FGF9_HUMAN    49 PAVTDLDHLKGILRRRQLYCRTGFHLEIFPNGTIQGTRKDHSRFGILEFISIAVGLVSIRGVDSGLYLGMNEKGELYGSEKLTQECVFREQFEENWYNTYSSNLYKHVDTGRRYYVALNKDGTPREGTRTKRHQKFTHFLPRPVDPDKVPELYKD 203
               SCOP domains d1g82d_ D: Fibroblast growth factor 9, FGF9                                                                                                                 SCOP domains
               CATH domains 1g82D00 D:49-203  [code=2.80.10.50, no name defined]                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.eeeeee....eeee.....eeee....hhhh.eeeeeee..eeeeee.....eeee.....eeee...hhhh.eeeeeee..eeeeeeeeee......eee..........hhhhh...hhhh.eeee..hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------V----N-------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------HBGF_FGF  PDB: D:122-145---------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: D:49-93 UniProt: 1-93         ----------------------------------Exon 1.4c  PDB: D:128-203 UniProt: 128-208 [INCOMPLETE]                      Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.3a  PDB: D:93-127           ---------------------------------------------------------------------------- Transcript 1 (2)
                 1g82 D  49 PAVTDLDHLKGILRRRQLYCRTGFHLEIFPNGTIQGTRKDHSRFGILEFISIAVGLVSIRGVDSGLYLGMNEKGELYGSEKLTQECVFREQFEENWYNTYSSNLYKHVDTGRRYYVALNKDGTPREGTRTKRHQKFTHFLPRPVDPDKVPELYKD 203
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198     

   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  (1, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1G82)

(-) Gene Ontology  (53, 53)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (FGF9_HUMAN | P31371)
molecular function
    GO:0016303    1-phosphatidylinositol-3-kinase activity    Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol + ATP = a 1-phosphatidyl-1D-myo-inositol 3-phosphate + ADP + 2 H(+).
    GO:0005088    Ras guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Ras superfamily. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0005104    fibroblast growth factor receptor binding    Interacting selectively and non-covalently with the fibroblast growth factor receptor (FGFR).
    GO:0008083    growth factor activity    The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    GO:0046934    phosphatidylinositol-4,5-bisphosphate 3-kinase activity    Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + ATP = a 1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate + ADP + 2 H(+).
    GO:0004713    protein tyrosine kinase activity    Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
    GO:0000165    MAPK cascade    An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0007267    cell-cell signaling    Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
    GO:0002062    chondrocyte differentiation    The process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte. A chondrocyte is a polymorphic cell that forms cartilage.
    GO:0048566    embryonic digestive tract development    The process whose specific outcome is the progression of the gut over time, from its formation to the mature structure during embryonic development. The gut is the region of the digestive tract extending from the beginning of the intestines to the anus.
    GO:0030326    embryonic limb morphogenesis    The process, occurring in the embryo, by which the anatomical structures of the limb are generated and organized. A limb is an appendage of an animal used for locomotion or grasping.
    GO:0048706    embryonic skeletal system development    The process, occurring during the embryonic phase, whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure.
    GO:0001654    eye development    The process whose specific outcome is the progression of the eye over time, from its formation to the mature structure. The eye is the organ of sight.
    GO:0008543    fibroblast growth factor receptor signaling pathway    The series of molecular signals generated as a consequence of a fibroblast growth factor receptor binding to one of its physiological ligands.
    GO:0042472    inner ear morphogenesis    The process in which the anatomical structures of the inner ear are generated and organized. The inner ear is the structure in vertebrates that contains the organs of balance and hearing. It consists of soft hollow sensory structures (the membranous labyrinth) containing fluid (endolymph) surrounded by fluid (perilymph) and encased in a bony cavity (the bony labyrinth). It consists of two chambers, the sacculus and utriculus, from which arise the cochlea and semicircular canals respectively.
    GO:0030324    lung development    The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax.
    GO:0060484    lung-associated mesenchyme development    The biological process whose specific outcome is the progression of a lung-associated mesenchyme from an initial condition to its mature state. This process begins with the formation of lung-associated mesenchyme and ends with the mature structure. Lung-associated mesenchyme is the tissue made up of loosely connected mesenchymal cells in the lung.
    GO:0008584    male gonad development    The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure.
    GO:0030238    male sex determination    The specification of male sex of an individual organism.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0030178    negative regulation of Wnt signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of the Wnt signaling pathway.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0001649    osteoblast differentiation    The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone.
    GO:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    GO:0046854    phosphatidylinositol phosphorylation    The process of introducing one or more phosphate groups into a phosphatidylinositol, any glycerophosphoinositol having one phosphatidyl group esterified to one of the hydroxy groups of inositol.
    GO:0036092    phosphatidylinositol-3-phosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of phosphatidylinositol-3-phosphate, a phosphatidylinositol monophosphate carrying the phosphate group at the 3-position.
    GO:0048015    phosphatidylinositol-mediated signaling    A series of molecular signals in which a cell uses a phosphatidylinositol-mediated signaling to convert a signal into a response. Phosphatidylinositols include phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0043410    positive regulation of MAPK cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade.
    GO:0032927    positive regulation of activin receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of the activity of any activin receptor signaling pathway.
    GO:0090263    positive regulation of canonical Wnt signaling pathway    Any process that increases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
    GO:0060045    positive regulation of cardiac muscle cell proliferation    Any process that activates or increases the frequency, rate or extent of cardiac muscle cell proliferation.
    GO:0051781    positive regulation of cell division    Any process that activates or increases the frequency, rate or extent of cell division.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0050679    positive regulation of epithelial cell proliferation    Any process that activates or increases the rate or extent of epithelial cell proliferation.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0002053    positive regulation of mesenchymal cell proliferation    The process of activating or increasing the rate or extent of mesenchymal cell proliferation. Mesenchymal cells are loosely organized embryonic cells.
    GO:0045880    positive regulation of smoothened signaling pathway    Any process that activates or increases the frequency, rate or extent of smoothened signaling.
    GO:0030949    positive regulation of vascular endothelial growth factor receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of vascular endothelial growth factor receptor signaling pathway activity.
    GO:0006606    protein import into nucleus    The directed movement of a protein from the cytoplasm to the nucleus.
    GO:0014066    regulation of phosphatidylinositol 3-kinase signaling    Any process that modulates the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
    GO:0048505    regulation of timing of cell differentiation    The process controlling the activation and/or rate at which relatively unspecialized cells acquire specialized features. Any process that modulates the rate, frequency or extent of the XXX at a consistent predetermined time point during its development.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0021762    substantia nigra development    The progression of the substantia nigra over time from its initial formation until its mature state. The substantia nigra is the layer of gray substance that separates the posterior parts of the cerebral peduncles (tegmentum mesencephali) from the anterior parts; it normally includes a posterior compact part with many pigmented cells (pars compacta) and an anterior reticular part whose cells contain little pigment (pars reticularis).
cellular component
    GO:0005604    basement membrane    A thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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