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(-) Description

Title :  CRYSTAL STRUCTURE OF PHOSPHORYLATED RET TYROSINE KINASE DOMAIN WITH INHIBITOR
 
Authors :  P. P. Knowles, J. Murray-Rust, S. Kjaer, N. Q. Mcdonald
Date :  13 Jan 10  (Deposition) - 09 Feb 10  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hirschsprung Disease, Gdnf Receptor, Transmembrane, Proto-Oncogene, Phosphoprotein, Disease Mutation, Phosphotransferase, Ret, Kinase, Membrane, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Mologni, R. Rostagno, S. Brussolo, P. P. Knowles, S. Kjaer, J. Murray-Rust, E. Rosso, A. Zambon, L. Scapozza, N. Q. Mcdonald, V. Lucchini, C. Gambacorti-Passerini
Synthesis, Structure-Activity Relationship And Crystallographic Studies Of 3-Substituted Indolin-2-One Ret Inhibitors.
Bioorg. Med. Chem. V. 18 1482 2010
PubMed-ID: 20117004  |  Reference-DOI: 10.1016/J.BMC.2010.01.011

(-) Compounds

Molecule 1 - PROTO-ONCOGENE TYROSINE-PROTEIN KINASE RECEPTOR RET
    ChainsA, B
    EC Number2.7.10.1
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF9
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPBACPAK-HIS3 (CLONTECH) MODIFIED
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    FragmentTYROSINE KINASE DOMAIN, RESIDUES 705-1013
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRET TYROSINE KINASE RECEPTOR, C-RET

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1FMT5Ligand/IonFORMIC ACID
2PTR2Mod. Amino AcidO-PHOSPHOTYROSINE
3X2M2Ligand/Ion(3Z)-3-[(3,5-DIMETHYL-1H-PYRROL-2-YL)METHYLIDENE]-1,3-DIHYDRO-2H-INDOL-2-ONE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:910 , LEU A:923 , HIS A:926 , GLY B:700 , PRO B:701 , LEU B:702 , SER B:703BINDING SITE FOR RESIDUE FMT B 2012
2AC2SOFTWAREARG A:873 , LEU A:895 , LYS A:907 , GLY A:911 , ARG A:912 , ILE A:913BINDING SITE FOR RESIDUE FMT A 2014
3AC3SOFTWAREGLY A:700 , LEU A:702 , SER A:703 , GLN B:910 , LEU B:923 , HIS B:926 , HOH B:3014BINDING SITE FOR RESIDUE FMT A 2015
4AC4SOFTWAREARG B:873 , LEU B:895 , LYS B:907 , GLY B:911 , ARG B:912 , ILE B:913BINDING SITE FOR RESIDUE FMT B 2013
5AC5SOFTWAREARG B:721 , CYS B:794 , ASP B:797 , GLY B:798 , PRO B:799 , LEU B:801BINDING SITE FOR RESIDUE FMT B 2014
6AC6SOFTWARELEU A:730 , ALA A:756 , LYS A:758 , VAL A:804 , GLU A:805 , TYR A:806 , ALA A:807 , LYS A:808 , GLY A:810 , LEU A:881 , SER A:891BINDING SITE FOR RESIDUE X2M A 2016
7AC7SOFTWARELEU B:730 , ALA B:756 , VAL B:804 , GLU B:805 , TYR B:806 , ALA B:807 , GLY B:810 , LEU B:881 , SER B:891BINDING SITE FOR RESIDUE X2M B 2015

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2X2M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2X2M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (30, 60)

Asymmetric/Biological Unit (30, 60)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_041765R749TRET_HUMANPolymorphism34288963A/BR749T
02UniProtVAR_009481E762QRET_HUMANDisease (HSCR1)  ---A/BE762Q
03UniProtVAR_009493S765PRET_HUMANDisease (HSCR1)75075748A/BS765P
04UniProtVAR_006334S767RRET_HUMANDisease (HSCR1)  ---A/BS767R
05UniProtVAR_006335E768DRET_HUMANDisease (MTC)78014899A/BE768D
06UniProtVAR_044395V778IRET_HUMANUnclassified75686697A/BV778I
07UniProtVAR_067119N783SRET_HUMANDisease (HSCR1)587778656A/BN783S
08UniProtVAR_009482L790FRET_HUMANDisease (MEN2A)75030001A/BL790F
09UniProtVAR_009483Y791FRET_HUMANDisease (PCC)77724903A/BY791F
10UniProtVAR_006336V804LRET_HUMANDisease (MTC)79658334A/BV804L
11UniProtVAR_006337V804MRET_HUMANDisease (MTC)79658334A/BV804M
12UniProtVAR_009484R813QRET_HUMANDisease (HSCR1)  ---A/BR813Q
13UniProtVAR_006338R873QRET_HUMANDisease (HSCR1)  ---A/BR873Q
14UniProtVAR_009485A883FRET_HUMANDisease (MEN2B)377767429A/BA883F
15UniProtVAR_009486S891ARET_HUMANDisease (MTC)75234356A/BS891A
16UniProtVAR_006339F893LRET_HUMANDisease (HSCR1)  ---A/BF893L
17UniProtVAR_044396G894SRET_HUMANUnclassified  ---A/BG894S
18UniProtVAR_006340R897QRET_HUMANDisease (HSCR1)76087194A/BR897Q
19UniProtVAR_006341K907ERET_HUMANDisease (HSCR1)377767430A/BK907E
20UniProtVAR_067121K907TRET_HUMANDisease (HSCR1)  ---A/BK907T
21UniProtVAR_006342M918TRET_HUMANDisease (MEN2B)74799832A/BM918T
22UniProtVAR_006343E921KRET_HUMANDisease (HSCR1)  ---A/BE921K
23UniProtVAR_012745S922FRET_HUMANDisease (MTC)377767432A/BS922F
24UniProtVAR_009487S922YRET_HUMANPolymorphism377767432A/BS922Y
25UniProtVAR_006345T946MRET_HUMANDisease (MEN2B)  ---A/BT946M
26UniProtVAR_067122F961LRET_HUMANDisease (HSCR1)  ---A/BF961L
27UniProtVAR_006346R972GRET_HUMANDisease (HSCR1)76534745A/BR972G
28UniProtVAR_006347P973LRET_HUMANDisease (HSCR1)  ---A/BP973L
29UniProtVAR_006348M980TRET_HUMANDisease (HSCR1)  ---A/BM980T
30UniProtVAR_006349R982CRET_HUMANPolymorphism17158558A/BR982C

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.RET_HUMAN730-758
 
  2A:730-758
B:730-758
2PROTEIN_KINASE_TYRPS00109 Tyrosine protein kinases specific active-site signature.RET_HUMAN870-882
 
  2A:870-882
B:870-882

(-) Exons   (8, 16)

Asymmetric/Biological Unit (8, 16)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003557101aENSE00001948565chr10:43572475-43572779305RET_HUMAN1-25250--
1.2ENST000003557102ENSE00001365997chr10:43595907-43596170264RET_HUMAN25-113890--
1.3ENST000003557103ENSE00001095923chr10:43597790-43598077288RET_HUMAN113-209970--
1.4bENST000003557104bENSE00001095946chr10:43600400-43600641242RET_HUMAN209-289810--
1.5bENST000003557105bENSE00001095907chr10:43601824-43602019196RET_HUMAN290-355660--
1.6ENST000003557106ENSE00001095904chr10:43604479-43604678200RET_HUMAN355-421670--
1.7ENST000003557107ENSE00001312192chr10:43606655-43606913259RET_HUMAN422-508870--
1.8ENST000003557108ENSE00001164816chr10:43607547-43607672126RET_HUMAN508-550430--
1.9ENST000003557109ENSE00001164807chr10:43608301-43608411111RET_HUMAN550-587380--
1.10ENST0000035571010ENSE00001164798chr10:43609004-43609123120RET_HUMAN587-627410--
1.11bENST0000035571011bENSE00001164787chr10:43609928-43610184257RET_HUMAN627-712862A:700-712 (gaps)
B:700-711 (gaps)
46
45
1.12ENST0000035571012ENSE00001095944chr10:43612032-43612179148RET_HUMAN713-762502A:714-762 (gaps)
B:715-762 (gaps)
49
48
1.13ENST0000035571013ENSE00001164770chr10:43613821-43613928108RET_HUMAN762-798372A:762-798
B:762-798
37
37
1.14ENST0000035571014ENSE00001164762chr10:43614979-43615193215RET_HUMAN798-869722A:798-869 (gaps)
B:798-869 (gaps)
72
72
1.15ENST0000035571015ENSE00001239109chr10:43615529-43615651123RET_HUMAN870-910412A:870-910
B:870-910
41
41
1.16ENST0000035571016ENSE00001095916chr10:43617394-4361746471RET_HUMAN911-934242A:911-934
B:911-934
24
24
1.17ENST0000035571017ENSE00001164739chr10:43619119-43619256138RET_HUMAN934-980472A:934-980
B:934-980
47
47
1.18ENST0000035571018ENSE00001164730chr10:43620331-43620430100RET_HUMAN980-1013342A:980-1013
B:980-1011
34
32
1.19aENST0000035571019aENSE00001095931chr10:43622023-43622170148RET_HUMAN1014-1063500--
1.20ENST0000035571020ENSE00001386034chr10:43623560-436257992240RET_HUMAN1063-1114520--

(-) Sequences/Alignments

Asymmetric/Biological 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:287
 aligned with RET_HUMAN | P07949 from UniProtKB/Swiss-Prot  Length:1114

    Alignment length:347
                                   676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886       896       906       916       926       936       946       956       966       976       986       996      1006       
           RET_HUMAN    667 PPISSAEMTFRRPAQAFPVSYSSSGARRPSLDSMENQVSVDAFKILEDPKWEFPRKNLVLGKTLGEGEFGKVVKATAFHLKGRAGYTTVAVKMLKENASPSELRDLLSEFNVLKQVNHPHVIKLYGACSQDGPLLLIVEYAKYGSLRGFLRESRKVGPGYLGSGGSRNSSSLDHPDERALTMGDLISFAWQISQGMQYLAEMKLVHRDLAARNILVAEGRKMKISDFGLSRDVYEEDSYVKRSQGRIPVKWMAIESLFDHIYTTQSDVWSFGVLLWEIVTLGGNPYPGIPPERLFNLLKTGHRMERPDNCSEEMYRLMLQCWKQEPDKRPVFADISKDLEKMMVKRR 1013
               SCOP domains d2x2                                 ma_ A: au tomated matches                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----                                 ---2x2mA0 1 A:707-806 Phospho  rylase Kinase; domain 1                                                 2x2mA02 A:807-                        1010 Transferase(Phosphotransferase) domain 1                                                                                                                         --- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh---------------------------------hhhh.....-......hhh.eeeeeeee.--..eeeeeeeeee..eeeeeeeeeee.....hhhhhhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhh..------------------------..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeee...eeee......ee......ee.......hhhhhhhhhhhhheehhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
             SAPs(SNPs) (1) ----------------------------------------------------------------------------------T------------Q--P-RD---------I----S------FF------------L--------Q-----------------------------------------------------------Q---------F-------A-LS--Q---------E----------T--KF-----------------------M--------------L----------GL------T-C------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------------------------------------------------------------------------------------M------------------------------------------------------------------------------------------------------T--------------Y------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ---------------------------------------------------------------PROTEIN_KINASE_ATP           ---------------------------------------------------------------------------------------------------------------PROTEIN_KINAS----------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.11b  PDB: A:700-712 (gaps) [INCOMPLETE]Exon 1.12  PDB: A:714-762 (gaps) UniProt: 713-762 -----------------------------------Exon 1.14  PDB: A:798-869 (gaps) UniProt: 798-869                       Exon 1.15  PDB: A:870-910                Exon 1.16  PDB: A:911-93---------------------------------------------Exon 1.18  PDB: A:980-1013         Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------Exon 1.13  PDB: A:762-798            ---------------------------------------------------------------------------------------------------------------------------------------Exon 1.17  PDB: A:934-980 UniProt: 934-980     --------------------------------- Transcript 1 (2)
                2x2m A  700 GPLS---------------------------------LSVDAFKIL-DPKWEFPRKNLVLGKTLGE--FGKVVKATAFHLKGRAGYTTVAVKMLKENASPSELRDLLSEFNVLKQVNHPHVIKLYGACSQDGPLLLIVEYAKYGSLRGFLRESR------------------------ALTMGDLISFAWQISQGMQYLAEMKLVHRDLAARNILVAEGRKMKISDFGLSRDVYEEDSyVKRSQGRIPVKWMAIESLFDHIYTTQSDVWSFGVLLWEIVTLGGNPYPGIPPERLFNLLKTGHRMERPDNCSEEMYRLMLQCWKQEPDKRPVFADISKDLEKMMVKRR 1013
                               |     -         -         -       706     | 716       726     | 736       746       756       766       776       786       796       806       816   |     -         -       846       856       866       876       886       896       906       916       926       936       946       956       966       976       986       996      1006       
                             703                               704     712 |               732  |                                                                                  820                      845                                                         905-PTR                                                                                                        
                                                                         714                  735                                                                                                                                                                                                                                                                                      

Chain B from PDB  Type:PROTEIN  Length:280
 aligned with RET_HUMAN | P07949 from UniProtKB/Swiss-Prot  Length:1114

    Alignment length:345
                                   676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886       896       906       916       926       936       946       956       966       976       986       996      1006     
           RET_HUMAN    667 PPISSAEMTFRRPAQAFPVSYSSSGARRPSLDSMENQVSVDAFKILEDPKWEFPRKNLVLGKTLGEGEFGKVVKATAFHLKGRAGYTTVAVKMLKENASPSELRDLLSEFNVLKQVNHPHVIKLYGACSQDGPLLLIVEYAKYGSLRGFLRESRKVGPGYLGSGGSRNSSSLDHPDERALTMGDLISFAWQISQGMQYLAEMKLVHRDLAARNILVAEGRKMKISDFGLSRDVYEEDSYVKRSQGRIPVKWMAIESLFDHIYTTQSDVWSFGVLLWEIVTLGGNPYPGIPPERLFNLLKTGHRMERPDNCSEEMYRLMLQCWKQEPDKRPVFADISKDLEKMMVK 1011
               SCOP domains d2x2                                 mb_ B: a   utomated matches                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ----                                 ---2x2mB   01 B:707-806 Phosp    horylase Kinase; domain 1                                             2x2mB02 B:807                         -1010 Transferase(Phosphotransferase) domain 1                                                                                                                        - CATH domains
           Pfam domains (1) ----                                 --------   ---------Pkinase_T    yr-2x2mB01 B:724-1005                                                                                                                                                                                                                                                        ------ Pfam domains (1)
           Pfam domains (2) ----                                 --------   ---------Pkinase_T    yr-2x2mB02 B:724-1005                                                                                                                                                                                                                                                        ------ Pfam domains (2)
         Sec.struct. author hhhh---------------------------------hhhh....---.....hhh.eeeeeeee.----.eeeeeee.......eeeeeeee.....hhhhhhhhhhhhhhhh.........eeeee......eeee......hhhhhhhh.-------------------------..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeee...eeee......ee......ee.......hhhhhhhhhhhhheehhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh Sec.struct. author
             SAPs(SNPs) (1) ----------------------------------------------------------------------------------T------------Q--P-RD---------I----S------FF------------L--------Q-----------------------------------------------------------Q---------F-------A-LS--Q---------E----------T--KF-----------------------M--------------L----------GL------T-C----------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------------------------------------------------------------------------------------M------------------------------------------------------------------------------------------------------T--------------Y----------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ---------------------------------------------------------------PROTEIN_KINASE_ATP           ---------------------------------------------------------------------------------------------------------------PROTEIN_KINAS--------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.11b  PDB: B:700-711 (gaps) [INCOMPLETE]Exon 1.12  PDB: B:715-762 (gaps) UniProt: 713-762 -----------------------------------Exon 1.14  PDB: B:798-869 (gaps) UniProt: 798-869                       Exon 1.15  PDB: B:870-910                Exon 1.16  PDB: B:911-93---------------------------------------------Exon 1.18  PDB: B:980-1011       Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------Exon 1.13  PDB: B:762-798            ---------------------------------------------------------------------------------------------------------------------------------------Exon 1.17  PDB: B:934-980 UniProt: 934-980     ------------------------------- Transcript 1 (2)
                2x2m B  700 GPLS---------------------------------LSVDAFKI---PKWEFPRKNLVLGKTLGE----KVVKATAFHLKGRAGYTTVAVKMLKENASPSELRDLLSEFNVLKQVNHPHVIKLYGACSQDGPLLLIVEYAKYGSLRGFLRES-------------------------ALTMGDLISFAWQISQGMQYLAEMKLVHRDLAARNILVAEGRKMKISDFGLSRDVYEEDSyVKRSQGRIPVKWMAIESLFDHIYTTQSDVWSFGVLLWEIVTLGGNPYPGIPPERLFNLLKTGHRMERPDNCSEEMYRLMLQCWKQEPDKRPVFADISKDLEKMMVK 1011
                               |     -         -         -       706    |  716       726     |   -|      746       756       766       776       786       796       806       816  |      -         -       846       856       866       876       886       896       906       916       926       936       946       956       966       976       986       996      1006     
                             703                               704    711 715              732  737                                                                               819                       845                                                         905-PTR                                                                                                      

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PKinase (934)

(-) Gene Ontology  (64, 64)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RET_HUMAN | P07949)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004713    protein tyrosine kinase activity    Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0004714    transmembrane receptor protein tyrosine kinase activity    Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate.
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:0061146    Peyer's patch morphogenesis    The process in which a Peyer's patch is generated and organized. Peyer's patches are typically found as nodules associated with gut epithelium with distinct internal structures including B- and T-zones for the activation of lymphocytes.
    GO:0006919    activation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0071300    cellular response to retinoic acid    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a retinoic acid stimulus.
    GO:0001838    embryonic epithelial tube formation    The morphogenesis of an embryonic epithelium into a tube-shaped structure.
    GO:0048484    enteric nervous system development    The process whose specific outcome is the progression of the enteric nervous system over time, from its formation to the mature structure. The enteric nervous system is composed of two ganglionated neural plexuses in the gut wall which form one of the three major divisions of the autonomic nervous system. The enteric nervous system innervates the gastrointestinal tract, the pancreas, and the gall bladder. It contains sensory neurons, interneurons, and motor neurons. Thus the circuitry can autonomously sense the tension and the chemical environment in the gut and regulate blood vessel tone, motility, secretions, and fluid transport. The system is itself governed by the central nervous system and receives both parasympathetic and sympathetic innervation.
    GO:0007156    homophilic cell adhesion via plasma membrane adhesion molecules    The attachment of a plasma membrane adhesion molecule in one cell to an identical molecule in an adjacent cell.
    GO:0060384    innervation    The process in which a nerve invades a tissue and makes functional synaptic connection within the tissue.
    GO:0097021    lymphocyte migration into lymphoid organs    The movement of a lymphocyte within the lymphatic system into lymphoid organs such as lymph nodes, spleen or Peyer's patches, and its subsequent positioning within defined functional compartments such as sites of cell activation by antigen.
    GO:0033619    membrane protein proteolysis    The proteolytic cleavage of a transmembrane protein leading to the release of its intracellular or ecto-domains.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0001755    neural crest cell migration    The characteristic movement of cells from the dorsal ridge of the neural tube to a variety of locations in a vertebrate embryo.
    GO:0007158    neuron cell-cell adhesion    The attachment of a neuron to another cell via adhesion molecules.
    GO:0030182    neuron differentiation    The process in which a relatively unspecialized cell acquires specialized features of a neuron.
    GO:0042551    neuron maturation    A developmental process, independent of morphogenetic (shape) change, that is required for a neuron to attain its fully functional state.
    GO:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0033630    positive regulation of cell adhesion mediated by integrin    Any process that activates or increases the frequency, rate, or extent of cell adhesion mediated by integrin.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0045793    positive regulation of cell size    Any process that increases cell size.
    GO:2001241    positive regulation of extrinsic apoptotic signaling pathway in absence of ligand    Any process that activates or increases the frequency, rate or extent of extrinsic apoptotic signaling pathway in absence of ligand.
    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:0072300    positive regulation of metanephric glomerulus development    Any process that increases the rate, frequency or extent of metanephric glomerulus development, the progression of the metanephric glomerulus over time from its initial formation until its mature state. The metanephric glomerulus is a capillary tuft surrounded by Bowman's capsule in nephrons of the vertebrate kidney, or metanephros.
    GO:0014042    positive regulation of neuron maturation    Any process that activates or increases the frequency, rate or extent of neuron maturation.
    GO:0010976    positive regulation of neuron projection development    Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007497    posterior midgut development    The process whose specific outcome is the progression of the posterior midgut over time, from its formation to the mature structure.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0050770    regulation of axonogenesis    Any process that modulates the frequency, rate or extent of axonogenesis, the generation of an axon, the long process of a neuron.
    GO:0030155    regulation of cell adhesion    Any process that modulates the frequency, rate or extent of attachment of a cell to another cell or to the extracellular matrix.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0048265    response to pain    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pain stimulus. Pain stimuli cause activation of nociceptors, peripheral receptors for pain, include receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli.
    GO:0060041    retina development in camera-type eye    The process whose specific outcome is the progression of the retina over time, from its formation to the mature structure. The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
    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:0007169    transmembrane receptor protein tyrosine kinase signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0035799    ureter maturation    A developmental process, independent of morphogenetic (shape) change, that is required for the ureter to attain its fully functional state. The ureter is a muscular tube that transports urine from the kidney to the urinary bladder or from the Malpighian tubule to the hindgut.
    GO:0001657    ureteric bud development    The process whose specific outcome is the progression of the ureteric bud over time, from its formation to the mature structure.
cellular component
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    GO:0005769    early endosome    A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0010008    endosome membrane    The lipid bilayer surrounding an endosome.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0043235    receptor complex    Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.

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 Related Entries

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

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        RET_HUMAN | P079491xpd 2ivs 2ivt 2ivu 2ivv 2x2k 2x2l 2x2u 4cki 4ckj 4ux8 5amn 5fm2 5fm3

(-) Related Entries Specified in the PDB File

2ivs CRYSTAL STRUCTURE OF NON-PHOSPHORYLATED RET TYROSINE KINASE DOMAIN
2ivt CRYSTAL STRUCTURE OF PHOSPHORYLATED RET TYROSINE KINASE DOMAIN
2ivu CRYSTAL STRUCTURE OF PHOSPHORYLATED RET TYROSINE KINASE DOMAIN COMPLEXED WITH THE INHIBITOR ZD6474
2ivv CRYSTAL STRUCTURE OF PHOSPHORYLATED RET TYROSINE KINASE DOMAIN COMPLEXED WITH THE INHIBITOR PP1
2x2k CRYSTAL STRUCTURE OF PHOSPHORYLATED RET TYROSINE KINASE DOMAIN WITH INHIBITOR
2x2l CRYSTAL STRUCTURE OF PHOSPHORYLATED RET TYROSINE KINASE DOMAIN WITH INHIBITOR