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(-) Description

Title :  CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF HUMAN GIP RECEPTOR IN COMPLEX WITH THE HORMONE GIP
 
Authors :  C. Parthier, M. Kleinschmidt, P. Neumann, R. Rudolph, S. Manhart, D. Schlenzig, J. Fanghanel, J. -U. Rahfeld, H. -U. Demuth, M. T. Stubbs
Date :  11 Jul 07  (Deposition) - 14 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Gpcr, Incretin, Hormone-Gpcr Complex, Extracellular Domain, Ligand Binding Domain, Ecd, Glugacon Receptor Family, Hormone Recognition Fold, Diabetes, Helix Formation, Cleavage On Pair Of Basic Residues, Polymorphism, Alternative Splicing, G-Protein Coupled Receptor, Glycoprotein, Membrane, Transducer, Transmembrane, Signaling Protein/Hormone Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Parthier, M. Kleinschmidt, P. Neumann, R. Rudolph, S. Manhart, D. Schlenzig, J. Fanghanel, J. -U. Rahfeld, H. -U. Demuth, M. T. Stubbs
Crystal Structure Of The Incretin-Bound Extracellular Domain Of A G Protein-Coupled Receptor
Proc. Natl. Acad. Sci. Usa V. 104 13942 2007
PubMed-ID: 17715056  |  Reference-DOI: 10.1073/PNAS.0706404104
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUCOSE-DEPENDENT INSULINOTROPIC POLYPEPTIDE
    ChainsB
    EngineeredYES
    FragmentSEQUENCE DATABASE RESIDUES 52-93
    Other DetailsTHE PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN).
    SynonymGASTRIC INHIBITORY POLYPEPTIDE, GIP
    SyntheticYES
 
Molecule 2 - GLUCOSE-DEPENDENT INSULINOTROPIC POLYPEPTIDE RECEPTOR
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET-28A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentEXTRACELLULAR DOMAIN, RESIDUES 29-138
    GeneGIPR
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGASTRIC INHIBITORY POLYPEPTIDE RECEPTOR, GIP-R

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1QKH1Ligand/IonMETHYL-CYCLO-HEPTA-AMYLOSE
2TAR1Ligand/IonD(-)-TARTARIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:32 , GLY A:33 , TYR A:36 , GLU A:48 , HOH A:226 , TYR B:1 , PHE B:6 , TYR B:10 , SER B:11 , HIS B:18 , PHE B:22 , HOH B:221 , HOH B:264 , HOH B:285BINDING SITE FOR RESIDUE QKH B 150
2AC2SOFTWAREGLN A:37 , ARG A:41 , ARG A:44 , HOH A:202BINDING SITE FOR RESIDUE TAR A 151

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:46 -A:70
2A:61 -A:103
3A:84 -A:118

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QKH)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_PROTEIN_RECEP_F2_3PS50227 G-protein coupled receptors family 2 profile 1.GIPR_HUMAN45-122  1A:45-122
2GLUCAGONPS00260 Glucagon / GIP / secretin / VIP family signature.GIP_HUMAN52-74  1B:1-23
3G_PROTEIN_RECEP_F2_1PS00649 G-protein coupled receptors family 2 signature 1.GIPR_HUMAN61-85  1A:61-85

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003574241ENSE00001192994chr17:47045958-4704587980GIP_HUMAN-00--
1.2ENST000003574242ENSE00001430288chr17:47044615-47044509107GIP_HUMAN1-29290--
1.3ENST000003574243ENSE00001044108chr17:47041842-47041672171GIP_HUMAN29-86581B:1-3232
1.4ENST000003574244ENSE00001044115chr17:47039181-4703908993GIP_HUMAN86-117320--
1.5ENST000003574245ENSE00001192996chr17:47038349-47038248102GIP_HUMAN117-151350--
1.6ENST000003574246ENSE00001192983chr17:47036078-47035916163GIP_HUMAN151-15330--

(-) 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:94
 aligned with GIPR_HUMAN | P48546 from UniProtKB/Swiss-Prot  Length:466

    Alignment length:94
                                    38        48        58        68        78        88        98       108       118    
           GIPR_HUMAN    29 GQTAGELYQRWERYRRECQETLAAAEPPSGLACNGSFDMYVCWDYAAPNATARASCPWYLPWHHHVAAGFVLRQCGSDGQWGLWRDHTQCENPE 122
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------HRM-2qkhA01 A:58-121                                            - Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh..........ee....ee......eeeeee......hhhhhh..eeeeee...........hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------G_PROTEIN_RECEP_F2_3  PDB: A:45-122 UniProt: 45-122                            PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) --------------------------------G_PROTEIN_RECEP_F2_1     ------------------------------------- PROSITE (3)
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 2qkh A  29 GQTAGELYQRWERYRRECQETLAAAEPPSGLACNGSFDMYVCWDYAAPNATARASCPWYLPWHHHVAAGFVLRQCGSDGQWGLWRDHTQCENPE 122
                                    38        48        58        68        78        88        98       108       118    

Chain B from PDB  Type:PROTEIN  Length:32
 aligned with GIP_HUMAN | P09681 from UniProtKB/Swiss-Prot  Length:153

    Alignment length:32
                                    61        71        81  
            GIP_HUMAN    52 YAEGTFISDYSIAMDKIHQQDFVNWLLAQKGK  83
               SCOP domains -------------------------------- SCOP domains
               CATH domains -------------------------------- CATH domains
               Pfam domains Hormone_2-2qkhB01 B:1-28    ---- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------- SAPs(SNPs)
                PROSITE (2) GLUCAGON  PDB: B:1-23  --------- PROSITE (2)
               Transcript 1 Exon 1.3  PDB: B:1-32            Transcript 1
                 2qkh B   1 YAEGTFISDYSIAMDKIHQQDFVNWLLAQKGK  32
                                    10        20        30  

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2QKH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2QKH)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (57, 63)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GIPR_HUMAN | P48546)
molecular function
    GO:0004930    G-protein coupled receptor activity    Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex.
    GO:0016519    gastric inhibitory peptide receptor activity    Combining with gastric inhibitory peptide (GIP) and transmitting the signal across the membrane to activate an associated G-protein.
    GO:0017046    peptide hormone binding    Interacting selectively and non-covalently with any peptide with hormonal activity in animals.
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
    GO:0004888    transmembrane signaling receptor activity    Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction.
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:0007190    activation of adenylate cyclase activity    Any process that initiates the activity of the inactive enzyme adenylate cyclase.
    GO:0007166    cell surface receptor signaling pathway    A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0002029    desensitization of G-protein coupled receptor protein signaling pathway    The process that stops, prevents, or reduces the frequency, rate or extent of G-protein coupled receptor protein signaling pathway activity after prolonged stimulation with an agonist of the pathway.
    GO:0031018    endocrine pancreas development    The process whose specific outcome is the progression of the endocrine pancreas over time, from its formation to the mature structure. The endocrine pancreas is made up of islet cells that produce insulin, glucagon and somatostatin.
    GO:0038192    gastric inhibitory peptide signaling pathway    The series of molecular signals generated as a consequence of a gastric inhibitory peptide (GIP) binding to a cell surface receptor. The pathway proceeds with the receptor transmitting the signal to a heterotrimeric G-protein complex and ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0006091    generation of precursor metabolites and energy    The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.
    GO:0030819    positive regulation of cAMP biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
    GO:0007204    positive regulation of cytosolic calcium ion concentration    Any process that increases the concentration of calcium ions in the cytosol.
    GO:0032024    positive regulation of insulin secretion    Any process that activates or increases the frequency, rate or extent of the regulated release of insulin.
    GO:0050796    regulation of insulin secretion    Any process that modulates the frequency, rate or extent of the regulated release of insulin.
    GO:0048678    response to axon injury    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 axon injury stimulus.
    GO:0051592    response to calcium ion    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 calcium ion stimulus.
    GO:0070542    response to fatty 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 fatty acid stimulus.
    GO:0009749    response to glucose    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 glucose stimulus.
    GO:0007584    response to nutrient    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 nutrient stimulus.
    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.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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 B   (GIP_HUMAN | P09681)
molecular function
    GO:0005179    hormone activity    The action characteristic of a hormone, any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action. The term was originally applied to agents with a stimulatory physiological action in vertebrate animals (as opposed to a chalone, which has a depressant action). Usage is now extended to regulatory compounds in lower animals and plants, and to synthetic substances having comparable effects; all bind receptors and trigger some biological process.
    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: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:0008344    adult locomotory behavior    Locomotory behavior in a fully developed and mature organism.
    GO:0055123    digestive system development    The process whose specific outcome is the progression of the digestive system over time, from its formation to the mature structure. The digestive system is the entire structure in which digestion takes place. Digestion is all of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
    GO:0031018    endocrine pancreas development    The process whose specific outcome is the progression of the endocrine pancreas over time, from its formation to the mature structure. The endocrine pancreas is made up of islet cells that produce insulin, glucagon and somatostatin.
    GO:0035640    exploration behavior    The specific behavior of an organism in response to a novel environment or stimulus.
    GO:0007565    female pregnancy    The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth.
    GO:0060291    long-term synaptic potentiation    A process that modulates synaptic plasticity such that synapses are changed resulting in the increase in the rate, or frequency of synaptic transmission at the synapse.
    GO:0007613    memory    The activities involved in the mental information processing system that receives (registers), modifies, stores, and retrieves informational stimuli. The main stages involved in the formation and retrieval of memory are encoding (processing of received information by acquisition), storage (building a permanent record of received information as a result of consolidation) and retrieval (calling back the stored information and use it in a suitable way to execute a given task).
    GO:0043950    positive regulation of cAMP-mediated signaling    Any process which activates, maintains or increases the frequency, rate or extent of cAMP-mediated signaling, a series of molecular signals in which a cell uses cyclic AMP to convert an extracellular signal into a response.
    GO:0070094    positive regulation of glucagon secretion    Any process that activates or increases the frequency, rate or extent of the regulated release of glucagon.
    GO:0010828    positive regulation of glucose transport    Any process that increases the frequency, rate or extent of glucose transport. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0032024    positive regulation of insulin secretion    Any process that activates or increases the frequency, rate or extent of the regulated release of insulin.
    GO:0050806    positive regulation of synaptic transmission    Any process that activates or increases the frequency, rate or extent of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse.
    GO:0050796    regulation of insulin secretion    Any process that modulates the frequency, rate or extent of the regulated release of insulin.
    GO:0010447    response to acidic pH    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 pH stimulus with pH < 7. pH is a measure of the acidity or basicity of an aqueous solution.
    GO:0043200    response to amino 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 an amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups.
    GO:0048678    response to axon injury    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 axon injury stimulus.
    GO:0009743    response to carbohydrate    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 carbohydrate stimulus.
    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:0009749    response to glucose    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 glucose stimulus.
    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:0031667    response to nutrient levels    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 reflecting the presence, absence, or concentration of nutrients.
    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:0043434    response to peptide hormone    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 peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals.
    GO:0010269    response to selenium ion    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 from selenium ion.
    GO:0042594    response to starvation    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 starvation stimulus, deprivation of nourishment.
    GO:0019233    sensory perception of pain    The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. Pain is medically defined as the physical sensation of discomfort or distress caused by injury or illness, so can hence be described as a harmful stimulus which signals current (or impending) tissue damage. Pain may come from extremes of temperature, mechanical damage, electricity or from noxious chemical substances. This is a neurological process.
    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:0070328    triglyceride homeostasis    Any process involved in the maintenance of an internal steady state of triglyceride within an organism or cell.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    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.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0034774    secretory granule lumen    The volume enclosed by the membrane of a secretory granule.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GIPR_HUMAN | P485464hj0
        GIP_HUMAN | P096811t5q 2b4n 2l70 2l71 2obu

(-) Related Entries Specified in the PDB File

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