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(-) Description

Title :  STRUCTURAL DETERMINANTS OF THE NHERF INTERACTION WITH BETA2-AR AND PDGFR
 
Authors :  S. Karthikeyan, T. Leung, J. A. A. Ladias
Date :  20 Nov 01  (Deposition) - 14 Nov 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Signaling Protein, Pdz, Beta2-Adrenergic Receptor, Pdgfr, Nherf, Crystal Structure, Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Karthikeyan, T. Leung, J. A. A. Ladias
Structural Determinants Of The Na+/H+ Exchanger Regulatory Factor Interaction With The Beta 2 Adrenergic And Platelet-Derived Growth Factor Receptors
J. Biol. Chem. V. 277 18973 2002
PubMed-ID: 11882663  |  Reference-DOI: 10.1074/JBC.M201507200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EZRIN-RADIXIN-MOESIN BINDING PHOSPHOPROTEIN-50
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-2T
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentPDZ1 DOMAIN, RESIDUES 11-94
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNA+/H+ EXCHANGER REGULATORY FACTOR

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:41 , ALA A:55 , HOH A:2014 , HOH A:2031BINDING SITE FOR RESIDUE CL A1100
2AC2SOFTWAREARG A:40 , VAL A:91 , ASP A:92 , HOH A:2003BINDING SITE FOR RESIDUE CL A1101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1GQ5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1GQ5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_067661E68ANHRF1_HUMANDisease (NPHLOP2)139622189AE68A

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.NHRF1_HUMAN14-94
154-234
  1A:14-94
-

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002617991aENSE00002153218chr5:149535423-149534960464PGFRB_HUMAN-00--
1.3ENST000002617993ENSE00001277271chr5:149516616-14951657146PGFRB_HUMAN1-14140--
1.4ENST000002617994ENSE00001277242chr5:149515441-149515118324PGFRB_HUMAN14-1221090--
1.5bENST000002617995bENSE00002159078chr5:149514579-149514313267PGFRB_HUMAN122-211900--
1.6bENST000002617996bENSE00001023107chr5:149513571-149513444128PGFRB_HUMAN211-253430--
1.7bENST000002617997bENSE00001277219chr5:149513323-149513149175PGFRB_HUMAN254-312590--
1.8ENST000002617998ENSE00001023111chr5:149512505-149512313193PGFRB_HUMAN312-376650--
1.9ENST000002617999ENSE00001023106chr5:149511657-149511542116PGFRB_HUMAN376-415400--
1.10ENST0000026179910ENSE00001277198chr5:149510225-149510102124PGFRB_HUMAN415-456420--
1.11ENST0000026179911ENSE00001277189chr5:149509531-149509320212PGFRB_HUMAN456-527720--
1.12ENST0000026179912ENSE00000767184chr5:149506177-14950608395PGFRB_HUMAN527-558320--
1.13aENST0000026179913aENSE00001277173chr5:149505140-149505008133PGFRB_HUMAN559-603450--
1.14aENST0000026179914aENSE00000972770chr5:149504394-149504290105PGFRB_HUMAN603-638360--
1.14cENST0000026179914cENSE00000767180chr5:149503923-149503813111PGFRB_HUMAN638-675380--
1.15ENST0000026179915ENSE00000767179chr5:149502764-149502605160PGFRB_HUMAN675-728540--
1.17bENST0000026179917bENSE00001277146chr5:149501603-149501443161PGFRB_HUMAN728-782550--
1.18ENST0000026179918ENSE00001277140chr5:149500885-149500767119PGFRB_HUMAN782-821400--
1.19bENST0000026179919bENSE00001277135chr5:149500573-149500451123PGFRB_HUMAN822-862411A:9-20 (gaps)25
1.20ENST0000026179920ENSE00000767175chr5:149499686-149499575112PGFRB_HUMAN863-900381A:21-29 (gaps)29
1.21ENST0000026179921ENSE00000767174chr5:149499129-149499030100PGFRB_HUMAN900-933341A:29-34 (gaps)22
1.22ENST0000026179922ENSE00001277123chr5:149498415-149498310106PGFRB_HUMAN933-968361A:35-439
1.23ENST0000026179923ENSE00000767172chr5:149497413-149497181233PGFRB_HUMAN969-1046781A:44-80 (gaps)54
1.24bENST0000026179924bENSE00001277266chr5:149495509-1494934002110PGFRB_HUMAN1046-1106611A:80-99 (gaps)61

(-) 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:91
 aligned with NHRF1_HUMAN | O14745 from UniProtKB/Swiss-Prot  Length:358

    Alignment length:91
                                    18        28        38        48        58        68        78        88        98 
         NHRF1_HUMAN      9 APLPRLCCLEKGPNGYGFHLHGEKGKLGQYIRLVEPGSPAEKAGLLAGDRLVEVNGENVEKETHQQVVSRIRAALNAVRLLVVDPETDEQL   99
               SCOP domains d1gq5a_ A: Na+/H+ exchanger regulatory factor, NHERF                                        SCOP domains
               CATH domains 1gq5A00 A:9-99  [code=2.30.42.10, no name defined]                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee........eee........eee.....hhhhhhh.....eeeee..ee....hhhhhhhhhhhh..eeeeeee........ Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------A------------------------------- SAPs(SNPs)
                    PROSITE -----PDZ  PDB: A:14-94 UniProt: 14-94                                                 ----- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                1gq5 A    9 GMLPRLCCLEKGPNGYGFHLHGEKGKLGQYIRLVEPGSPAEKAGLLAGDRLVEVNGENVEKETHQQVVSRIRAALNAVRLLVVDPEEDSFL   99
                                    18        28        38        48        58        68        78        88        98 

Chain A from PDB  Type:PROTEIN  Length:91
 aligned with PGFRB_HUMAN | P09619 from UniProtKB/Swiss-Prot  Length:1106

    Alignment length:270
                                   846       856       866       876       886       896       906       916       926       936       946       956       966       976       986       996      1006      1016      1026      1036      1046      1056      1066      1076      1086      1096      1106
         PGFRB_HUMAN    837 GKLVKICDFGLARDIMRDSNYISKGSTFLPLKWMAPESIFNSLYTTLSDVWSFGILLWEIFTLGGTPYPELPMNEQFYNAIKRGYRMAQPAHASDEIYEIMQKCWEEKFEIRPPFSQLVLLLERLLGEGYKKKYQQVDEEFLRSDHPAILRSQARLPGFHGLRSPLDTSSVLYTAVQPNEGDNDYIIPLPDPKPEVADEGPLEGSPSLASSTLNEVNTSSTISCDSPLEPQDEPEPEPQLELQVEPEPELEQLPDSGCPAPRAEAEDSFL 1106
               SCOP domains d1gq5a_              A: N          a+              /H+       exch                ange                             r regulat                                 or     y factor,        NHE     RF                                                                                 SCOP domains
               CATH domains 1gq5A00              A:9-          99                [      code=                2.30                             .42.10, n                                 o      name defi       ned]                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee-------------eee..----------..--------------...------.eee.----------------....-----------------------------...eee...---------------------------------..-----hhhhhhh..-------...e-----eeee..ee....hhhhhhhhhhhh..eee-----------------------eeee...------------------..... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.19b [INCOMPLETE]   Exon 1.20  PDB: A:21-29 (gaps)        --------------------------------Exon 1.22  PDB: A:35-43 [INCOMPLETE]Exon 1.23  PDB: A:44-80 (gaps) UniProt: 969-1046 [INCOMPLETE]                 ------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------Exon 1.21  PDB: A:29-34 (gaps)    ----------------------------------------------------------------------------------------------------------------Exon 1.24b  PDB: A:80-99 (gaps) UniProt: 1046-1106            Transcript 1 (2)
                1gq5 A    9 GMLPRLC-------------CLEKG----------PN--------------GYG------FHLHG----------------EKGK-----------------------------LGQYIRLVE---------------------------------PG-----SPAEKAGLL-------AGDR-----LVEVNGENVEKETHQQVVSRIRAALNAVR-----------------------LLVVDPE------------------EDSFL   99
                                  |  -         -|   |    -     ||  -         - | |     -|   |    -         - |  |    -         -         -    |   40  |      -         -         -      || -   |    52 |      55  |     60        70        80      |  -         -         -|     |  -         -     |  99
                                 15            16  20         21|             23 |     26  30               31 34                            35      43                                44|    46      54      55 58    59                          87                      88    94                 95    
                                                               22               25                                                                                                      45                                                                                                                

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GQ5)

(-) Gene Ontology  (185, 237)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PGFRB_HUMAN | P09619)
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: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:0043548    phosphatidylinositol 3-kinase binding    Interacting selectively and non-covalently with a phosphatidylinositol 3-kinase, any enzyme that catalyzes the addition of a phosphate group to an inositol lipid at the 3' position of the inositol ring.
    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:0004992    platelet activating factor receptor activity    Combining with platelet activating factor to initiate a change in cell activity.
    GO:0005019    platelet-derived growth factor beta-receptor activity    Combining with platelet-derived growth factor isoform PDGF-BB or PDGF-AB to initiate a change in cell activity.
    GO:0048407    platelet-derived growth factor binding    Interacting selectively and non-covalently with platelet-derived growth factor.
    GO:0005161    platelet-derived growth factor receptor binding    Interacting selectively and non-covalently with the platelet-derived growth factor receptor.
    GO:0005017    platelet-derived growth factor-activated receptor activity    Combining with platelet-derived growth factor and transmitting the signal across the plasma membrane to initiate a change in cell activity.
    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:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    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.
    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.
    GO:0038085    vascular endothelial growth factor binding    Interacting selectively and non-covalently with a vascular endothelial growth factor.
biological process
    GO:0007186    G-protein coupled receptor signaling pathway    A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
    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:0035909    aorta morphogenesis    The process in which the anatomical structures of an aorta are generated and organized. An aorta is an artery that carries blood from the heart to other parts of the body.
    GO:0055003    cardiac myofibril assembly    The process whose specific outcome is the progression of the cardiac myofibril over time, from its formation to the mature structure. A cardiac myofibril is a myofibril specific to cardiac muscle cells.
    GO:0060326    cell chemotaxis    The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0060981    cell migration involved in coronary angiogenesis    The orderly movement of a cell from one site to another that will contribute to the formation of new blood vessels in the heart from pre-existing blood vessels.
    GO:0035441    cell migration involved in vasculogenesis    The orderly movement of a cell from one site to another that will contribute to the differentiation of an endothelial cell that will form de novo blood vessels and tubes.
    GO:0036120    cellular response to platelet-derived growth factor stimulus    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 platelet-derived growth factor stimulus.
    GO:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0006024    glycosaminoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of glycosaminoglycans, any of a group of polysaccharides that contain amino sugars.
    GO:0048839    inner ear development    The process whose specific outcome is the progression of the inner ear over time, from its formation to the mature structure.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0072284    metanephric S-shaped body morphogenesis    The process in which the metanephric S-shaped body is generated and organized. The metanephric S-shaped body is the successor of the metanephric comma-shaped body that contributes to the morphogenesis of a nephron in the metanephros.
    GO:0072278    metanephric comma-shaped body morphogenesis    The process in which the metanephric comma-shaped body is generated and organized. The metanephric comma-shaped body is the precursor structure to the metanephric S-shaped body that contributes to the morphogenesis of a nephron in the metanephros.
    GO:0072277    metanephric glomerular capillary formation    The process that gives rise to a metanephric glomerular capillary. This process pertains to the initial formation of a structure from unspecified parts.
    GO:0072262    metanephric glomerular mesangial cell proliferation involved in metanephros development    The multiplication or reproduction of glomerular mesangial cells in the metanephros, resulting in the expansion of the population.
    GO:0072275    metanephric glomerulus morphogenesis    The process in which the anatomical structures of the metanephric glomerulus are generated and organized. The metanephric glomerulus is a capillary tuft surrounded by Bowman's capsule in nephrons of the vertebrate kidney, or metanephros.
    GO:0035789    metanephric mesenchymal cell migration    The orderly movement of undifferentiated metanephric mesenchymal cells (precursors to metanephric mesangial cells) from the mesenchyme into the cleft of the developing glomerulus, during development of the metanephros.
    GO:0072075    metanephric mesenchyme development    The biological process whose specific outcome is the progression of a metanephric mesenchyme from an initial condition to its mature state. This process begins with the formation of metanephric mesenchyme and ends with the mature structure. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros.
    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:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    GO:0046488    phosphatidylinositol metabolic process    The chemical reactions and pathways involving phosphatidylinositol, any glycophospholipid in which a sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol.
    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: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: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:0048008    platelet-derived growth factor receptor signaling pathway    The series of molecular signals generated as a consequence of a platelet-derived growth factor receptor binding to one of its physiological ligands.
    GO:0035791    platelet-derived growth factor receptor-beta signaling pathway    A series of molecular signals initiated by the binding of a ligand to a beta-type platelet-derived growth factor receptor (PDGFbeta) on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:2000573    positive regulation of DNA biosynthetic process    Any process that activates or increases the frequency, rate or extent of DNA biosynthetic process.
    GO:0070374    positive regulation of ERK1 and ERK2 cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0043406    positive regulation of MAP kinase activity    Any process that activates or increases the frequency, rate or extent of MAP kinase activity.
    GO:0090280    positive regulation of calcium ion import    Any process that increases the rate, frequency, or extent of the directed movement of calcium ions into a cell or organelle.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0038091    positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway    A series of molecular signals initiated by the binding of a vascular endothelial growth factor (VEGF) to a platelet-derived growth factor receptor (PDGFR) on the surface of a cell, which activates or increases the frequency, rate or extent of cell proliferation.
    GO:0050921    positive regulation of chemotaxis    Any process that activates or increases the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient.
    GO:0032967    positive regulation of collagen biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals.
    GO:0035793    positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway    Any process that increases the frequency, rate or extent of metanephric mesenchymal cell migration as a result of the series of molecular signals generated as a consequence of a platelet-derived growth factor receptor-beta binding to one of its physiological ligands.
    GO:0045840    positive regulation of mitotic nuclear division    Any process that activates or increases the frequency, rate or extent of mitosis.
    GO:0043552    positive regulation of phosphatidylinositol 3-kinase activity    Any process that activates or increases the frequency, rate or extent of phosphatidylinositol 3-kinase activity.
    GO:0014068    positive regulation of phosphatidylinositol 3-kinase signaling    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
    GO:0010863    positive regulation of phospholipase C activity    Any process that increases the rate of phospholipase C activity.
    GO:0032516    positive regulation of phosphoprotein phosphatase activity    Any process that activates or increases the activity of a phosphoprotein phosphatase.
    GO:2000379    positive regulation of reactive oxygen species metabolic process    Any process that activates or increases the frequency, rate or extent of reactive oxygen species metabolic process.
    GO:0014911    positive regulation of smooth muscle cell migration    Any process that activates, maintains or increases the frequency, rate or extent of smooth muscle cell migration.
    GO:0048661    positive regulation of smooth muscle cell proliferation    Any process that activates or increases the rate or extent of smooth muscle cell proliferation.
    GO:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0032956    regulation of actin cytoskeleton organization    Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
    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:0032355    response to estradiol    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 stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
    GO:0043627    response to estrogen    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 stimulus by an estrogen, C18 steroid hormones that can stimulate the development of female sexual characteristics.
    GO:0034405    response to fluid shear stress    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 fluid shear stress stimulus. Fluid shear stress is the force acting on an object in a system where the fluid is moving across a solid surface.
    GO:0042542    response to hydrogen peroxide    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 hydrogen peroxide (H2O2) stimulus.
    GO:0055093    response to hyperoxia    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 stimulus indicating increased oxygen tension.
    GO:0033993    response to lipid    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 lipid stimulus.
    GO:0014070    response to organic cyclic compound    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 an organic cyclic compound stimulus.
    GO:0032526    response to retinoic acid    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 retinoic acid stimulus.
    GO:0009636    response to toxic substance    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 toxic stimulus.
    GO:0061298    retina vasculature development in camera-type eye    The process whose specific outcome is the progression of the vasculature of the retina over time, from its formation to the mature structure.
    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:0071670    smooth muscle cell chemotaxis    The directed movement of a smooth muscle cell in response to an external stimulus.
    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:0042060    wound healing    The series of events that restore integrity to a damaged tissue, following an injury.
cellular component
    GO:0016324    apical plasma membrane    The region of the plasma membrane located at the apical end of the cell.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    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:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    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:0031226    intrinsic component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane.
    GO:0043202    lysosomal lumen    The volume enclosed within the lysosomal membrane.
    GO:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    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.

Chain A   (NHRF1_HUMAN | O14745)
molecular function
    GO:0030165    PDZ domain binding    Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins.
    GO:0031698    beta-2 adrenergic receptor binding    Interacting selectively and non-covalently with a beta-2 adrenergic receptor.
    GO:0008013    beta-catenin binding    Interacting selectively and non-covalently with the beta subunit of the catenin complex.
    GO:0017081    chloride channel regulator activity    Modulates the activity of a chloride channel.
    GO:0050780    dopamine receptor binding    Interacting selectively and non-covalently with a dopamine receptor.
    GO:0070851    growth factor receptor binding    Interacting selectively and non-covalently with a growth factor receptor.
    GO:0019902    phosphatase binding    Interacting selectively and non-covalently with any phosphatase.
    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:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0032947    protein complex scaffold activity    A structural molecule activity that provides a physical support for the assembly of a multiprotein complex. The scaffold may or may not be part of the final complex.
    GO:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0043621    protein self-association    Interacting selectively and non-covalently with a domain within the same polypeptide.
    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:0016055    Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
    GO:0030036    actin cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0007191    adenylate cyclase-activating dopamine receptor signaling pathway    The series of molecular signals generated as a consequence of a dopamine receptor binding to its physiological ligand, where the pathway proceeds with activation of adenylyl cyclase and a subsequent increase in the concentration of cyclic AMP (cAMP).
    GO:0060088    auditory receptor cell stereocilium organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a stereocilium. A stereocilium is an actin-based protrusion from the apical surface of auditory hair cells.
    GO:0032782    bile acid secretion    The regulated release of bile acid, composed of any of a group of steroid carboxylic acids occurring in bile, by a cell or a tissue.
    GO:0019933    cAMP-mediated signaling    Any intracellular signal transduction in which the signal is passed on within the cell via cyclic AMP (cAMP). Includes production of cAMP, and downstream effectors that further transmit the signal within the cell.
    GO:0030643    cellular phosphate ion homeostasis    Any process involved in the maintenance of an internal steady state of phosphate ions at the level of a cell.
    GO:0034613    cellular protein localization    Any process in which a protein is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell.
    GO:0051683    establishment of Golgi localization    The directed movement of the Golgi to a specific location.
    GO:0045198    establishment of epithelial cell apical/basal polarity    The specification and formation of the apicobasal polarity of an epithelial cell.
    GO:0040023    establishment of nucleus localization    The directed movement of the nucleus to a specific location within a cell.
    GO:0090002    establishment of protein localization to plasma membrane    The directed movement of a protein to a specific location in the plasma membrane.
    GO:0022612    gland morphogenesis    The process in which the anatomical structures of a gland are generated and organized.
    GO:0034635    glutathione transport    The directed movement of glutathione, the tripeptide glutamylcysteinylglycine, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0030033    microvillus assembly    Formation of a microvillus, a thin cylindrical membrane-covered projection on the surface of a cell.
    GO:0070373    negative regulation of ERK1 and ERK2 cascade    Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0035414    negative regulation of catenin import into nucleus    Any process that decreases the rate, frequency or extent of the directed movement of a catenin protein from the cytoplasm into the nucleus.
    GO:0030336    negative regulation of cell migration    Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration.
    GO:2000146    negative regulation of cell motility    Any process that stops, prevents, or reduces the frequency, rate or extent of cell motility.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0045930    negative regulation of mitotic cell cycle    Any process that stops, prevents or reduces the rate or extent of progression through the mitotic cell cycle.
    GO:0014067    negative regulation of phosphatidylinositol 3-kinase signaling    Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
    GO:0010642    negative regulation of platelet-derived growth factor receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of the platelet-derived growth factor receptor signaling pathway.
    GO:0051898    negative regulation of protein kinase B signaling    Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase B signaling, a series of reactions mediated by the intracellular serine/threonine kinase protein kinase B.
    GO:0010766    negative regulation of sodium ion transport    Any process that decreases the frequency, rate or extent of the directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0032416    negative regulation of sodium:proton antiporter activity    Any process that stops or reduces the activity of a sodium:hydrogen antiporter, which catalyzes the reaction: Na+(out) + H+(in) = Na+(in) + H+(out).
    GO:0060158    phospholipase C-activating dopamine receptor signaling pathway    The series of molecular signals generated as a consequence of a dopamine receptor binding to its physiological ligand, where the pathway proceeds with activation of phospholipase C (PLC) and a subsequent release of inositol trisphosphate (IP3) and diacylglycerol (DAG).
    GO:2001244    positive regulation of intrinsic apoptotic signaling pathway    Any process that activates or increases the frequency, rate or extent of intrinsic apoptotic signaling pathway.
    GO:0006461    protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0008361    regulation of cell size    Any process that modulates the size of a cell.
    GO:0044062    regulation of excretion    Any process that modulates the frequency, rate, or extent of excretion, the elimination by an organism of the waste products that arise as a result of metabolic activity.
    GO:0045859    regulation of protein kinase activity    Any process that modulates the frequency, rate or extent of protein kinase activity.
    GO:0032415    regulation of sodium:proton antiporter activity    Any process that modulates the activity of a sodium:hydrogen antiporter, which catalyzes the reaction: Na+(out) + H+(in) = Na+(in) + H+(out).
    GO:0070293    renal absorption    A renal system process in which water, ions, glucose and proteins are taken up from the collecting ducts, glomerulus and proximal and distal loops of the nephron. In non-mammalian species, absorption may occur in related structures (e.g. protein absorption is observed in nephrocytes in Drosophila, see PMID:23264686).
    GO:0097291    renal phosphate ion absorption    A renal system process in which phosphate ions are taken up from the collecting ducts and proximal and distal loops of the nephron. In non-mammalian species, absorption may occur in related structures.
    GO:0003096    renal sodium ion transport    The directed movement of sodium ions (Na+) by the kidney.
    GO:0007605    sensory perception of sound    The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.
cellular component
    GO:0015629    actin cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
    GO:0045177    apical part of cell    The region of a polarized cell that forms a tip or is distal to a base. For example, in a polarized epithelial cell, the apical region has an exposed surface and lies opposite to the basal lamina that separates the epithelium from other tissue.
    GO:0016324    apical plasma membrane    The region of the plasma membrane located at the apical end of the cell.
    GO:0031526    brush border membrane    The portion of the plasma membrane surrounding the brush border.
    GO:0071944    cell periphery    The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005813    centrosome    A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0012505    endomembrane system    A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
    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:0030175    filopodium    Thin, stiff, actin-based protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal or dendritic growth cone, or a dendritic shaft.
    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:0005902    microvillus    Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells.
    GO:0031528    microvillus membrane    The portion of the plasma membrane surrounding a microvillus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    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:0001726    ruffle    Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.
    GO:0097225    sperm midpiece    The highly organized segment of the sperm flagellum which begins at the connecting piece and is characterized by the presence of 9 outer dense fibers (ODFs) that lie outside each of the 9 outer axonemal microtubule doublets and by a sheath of mitochondria that encloses the ODFs and the axoneme; the midpiece terminates about one-fourth of the way down the sperm flagellum at the annulus, which marks the beginning of the principal piece.
    GO:0032420    stereocilium    An actin-based protrusion from the apical surface of auditory and vestibular hair cells and of neuromast cells. These protrusions are supported by a bundle of cross-linked actin filaments (an actin cable), oriented such that the plus (barbed) ends are at the tip of the protrusion, capped by a tip complex which bridges to the plasma. Bundles of stereocilia act as mechanosensory organelles.
    GO:0032426    stereocilium tip    A distinct compartment at the tip of a stereocilium, distal to the site of attachment to the apical cell surface. It consists of a dense matrix bridging the barbed ends of the stereocilium actin filaments with the overlying plasma membrane, is dynamic compared to the shaft, and is required for stereocilium elongation.
    GO:0031982    vesicle    Any small, fluid-filled, spherical organelle enclosed by membrane.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NHRF1_HUMAN | O147451g9o 1gq4 1i92 1sgh 2d10 2jxo 2kjd 2krg 2m0t 2m0u 2m0v 2ozf 4jl7 4lmm 4mpa 4n6x 4pqw 4q3h
        PGFRA_HUMAN | P162345k5x
        PGFRB_HUMAN | P096191h9o 1lwp 1sha 2l6w 2pld 2ple 3mjg

(-) Related Entries Specified in the PDB File

1g9o FIRST PDZ DOMAIN OF THE HUMAN NA+/H+ EXCHANGER REGULATORY FACTOR
1gq5 STRUCTURAL DETERMINANTS OF THE NHERF INTERACTION WITH BETA2AR AND PDGFR
1i92 STRUCTURAL BASIS OF THE NHERF PDZ1-CFTR INTERACTION
1lwp BETA PLATELET-DERIVED GROWTH FACTOR RECEPTOR