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(-) Description

Title :  EVH1 DOMAIN FROM MURINE HOMER 2B/VESL 2
 
Authors :  M. Barzik, U. D. Carl, W. -D. Schubert, J. Wehland, D. W. Heinz
Date :  08 Mar 01  (Deposition) - 22 Aug 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.24
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,E  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  B (1x),D (1x),E (1x)
Biol. Unit 6:  A (1x),C (1x)
Biol. Unit 7:  A (1x),C (1x),E (1x)
Biol. Unit 8:  B (1x),D (1x)
Biol. Unit 9:  E  (1x)
Biol. Unit 10:  B,E  (1x)
Biol. Unit 11:  A  (1x)
Keywords :  Evh1 Domain, Homer, Vesl, X-Ray Crystal Structure, Brain, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Barzik, U. D. Carl, W. D. Schubert, R. Frank, J. Wehland, D. W. Heinz
The N-Terminal Domain Of Homer/Vesl Is A New Class Ii Evh1 Domain.
J. Mol. Biol. V. 309 155 2001
PubMed-ID: 11491285  |  Reference-DOI: 10.1006/JMBI.2001.4640
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HOMER 2B
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-6P-1
    Expression System StrainBL21 CODON +
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentEVH1 DOMAIN (N-TERMINAL)
    OrganBRAIN
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymHOMER 2B/VESL 2
 
Molecule 2 - PHE-ALA-PHE
    ChainsE
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit ABCDE
Biological Unit 1 (1x)A   E
Biological Unit 2 (1x) B   
Biological Unit 3 (1x)  C  
Biological Unit 4 (1x)   D 
Biological Unit 5 (1x) B (1x) D (1x)E (1x)
Biological Unit 6 (1x)A (1x) C (1x)  
Biological Unit 7 (1x)A (1x) C (1x) E (1x)
Biological Unit 8 (1x) B (1x) D (1x) 
Biological Unit 9 (1x)    E
Biological Unit 10 (1x) B  E
Biological Unit 11 (1x)A    

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1FLC2Ligand/IonCITRATE ANION
2PHE3Mod. Amino AcidPHENYLALANINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1FLC1Ligand/IonCITRATE ANION
2PHE1Mod. Amino AcidPHENYLALANINE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1FLC1Ligand/IonCITRATE ANION
2PHE1Mod. Amino AcidPHENYLALANINE
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1FLC-1Ligand/IonCITRATE ANION
2PHE-1Mod. Amino AcidPHENYLALANINE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1FLC-1Ligand/IonCITRATE ANION
2PHE1Mod. Amino AcidPHENYLALANINE
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
1FLC-1Ligand/IonCITRATE ANION
2PHE-1Mod. Amino AcidPHENYLALANINE
Biological Unit 6 (2, 2)
No.NameCountTypeFull Name
1FLC1Ligand/IonCITRATE ANION
2PHE1Mod. Amino AcidPHENYLALANINE
Biological Unit 7 (0, 0)
No.NameCountTypeFull Name
1FLC-1Ligand/IonCITRATE ANION
2PHE-1Mod. Amino AcidPHENYLALANINE
Biological Unit 8 (2, 2)
No.NameCountTypeFull Name
1FLC1Ligand/IonCITRATE ANION
2PHE1Mod. Amino AcidPHENYLALANINE
Biological Unit 9 (0, 0)
No.NameCountTypeFull Name
1FLC-1Ligand/IonCITRATE ANION
2PHE-1Mod. Amino AcidPHENYLALANINE
Biological Unit 10 (2, 2)
No.NameCountTypeFull Name
1FLC1Ligand/IonCITRATE ANION
2PHE1Mod. Amino AcidPHENYLALANINE
Biological Unit 11 (2, 2)
No.NameCountTypeFull Name
1FLC1Ligand/IonCITRATE ANION
2PHE1Mod. Amino AcidPHENYLALANINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:42 , ARG A:46 , ASN A:58 , ARG A:81 , ALA A:82 , HOH A:411BINDING SITE FOR RESIDUE FLC A 301
2AC2SOFTWAREASN A:83 , ARG B:42 , ARG B:46 , THR B:60 , ARG B:81BINDING SITE FOR RESIDUE FLC B 302
3AC3SOFTWARELYS C:73 , TRP D:24 , THR D:70 , PHE D:74BINDING SITE FOR RESIDUE PHE D 401
4AC4SOFTWARETHR A:33 , HOH A:420 , HOH A:428BINDING SITE FOR RESIDUE PHE A 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1I7A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1I7A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1I7A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1I7A)

(-) Exons   (0, 0)

(no "Exon" information available for 1I7A)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:103
 aligned with HOME2_MOUSE | Q9QWW1 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:109
                                    12        22        32        42        52        62        72        82        92       102         
          HOME2_MOUSE     3 EQPIFTTRAHVFQIDPSTKKNWVPASKQAVTVSYFYDVTRNSYRIISVDGAKVIINSTITPNMTFTKTSQKFGQWADSRANTVFGLGFSSELQLTKFAEKFQEVREAAR 111
               SCOP domains d1i7aa_ A: Hom      er                                                                                        SCOP domains
               CATH domains 1i7aA00 A:3-11      1 Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee.------..ee.....eeeeeeee....eeeeeeee..eeeeeeee.....eee....eeeeee....eeeeee..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 1i7a A   3 EQPIFTTRAHVFQI------NWVPASKQAVTVSYFYDVTRNSYRIISVDGAKVIINSTITPNMTFTKTSQKFGQWADSRANTVFGLGFSSELQLTKFAEKFQEVREAAR 111
                                    12   |     -|       32        42        52        62        72        82        92       102         
                                        16     23                                                                                        

Chain B from PDB  Type:PROTEIN  Length:103
 aligned with HOME2_MOUSE | Q9QWW1 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:109
                                    12        22        32        42        52        62        72        82        92       102         
          HOME2_MOUSE     3 EQPIFTTRAHVFQIDPSTKKNWVPASKQAVTVSYFYDVTRNSYRIISVDGAKVIINSTITPNMTFTKTSQKFGQWADSRANTVFGLGFSSELQLTKFAEKFQEVREAAR 111
               SCOP domains d1i7ab_ B: Hom      er                                                                                        SCOP domains
               CATH domains 1i7aB00 B:3-11      1 Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee------..ee.....eeeeeeee....eeeeeeee..eeeeeee......eee....eeeeeehhhheeeeee..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 1i7a B   3 EQPIFTTRAHVFQI------NWVPASKQAVTVSYFYDVTRNSYRIISVDGAKVIINSTITPNMTFTKTSQKFGQWADSRANTVFGLGFSSELQLTKFAEKFQEVREAAR 111
                                    12   |     -|       32        42        52        62        72        82        92       102         
                                        16     23                                                                                        

Chain C from PDB  Type:PROTEIN  Length:103
 aligned with HOME2_MOUSE | Q9QWW1 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:109
                                    12        22        32        42        52        62        72        82        92       102         
          HOME2_MOUSE     3 EQPIFTTRAHVFQIDPSTKKNWVPASKQAVTVSYFYDVTRNSYRIISVDGAKVIINSTITPNMTFTKTSQKFGQWADSRANTVFGLGFSSELQLTKFAEKFQEVREAAR 111
               SCOP domains d1i7ac_ C: Hom      er                                                                                        SCOP domains
               CATH domains 1i7aC00 C:3-11      1 Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee------..ee.....eeeeeeee....eeeeeeee..eeeeeee......eeeee..eeeeee....eeeeeee.hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 1i7a C   3 EQPIFTTRAHVFQI------NWVPASKQAVTVSYFYDVTRNSYRIISVDGAKVIINSTITPNMTFTKTSQKFGQWADSRANTVFGLGFSSELQLTKFAEKFQEVREAAR 111
                                    12   |     -|       32        42        52        62        72        82        92       102         
                                        16     23                                                                                        

Chain D from PDB  Type:PROTEIN  Length:104
 aligned with HOME2_MOUSE | Q9QWW1 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:110
                                    12        22        32        42        52        62        72        82        92       102       112
          HOME2_MOUSE     3 EQPIFTTRAHVFQIDPSTKKNWVPASKQAVTVSYFYDVTRNSYRIISVDGAKVIINSTITPNMTFTKTSQKFGQWADSRANTVFGLGFSSELQLTKFAEKFQEVREAARL 112
               SCOP domains d1i7ad_ D: Hom      er                                                                                         SCOP domains
               CATH domains 1i7aD00 D:3-11      1 Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)            - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee------..ee.....eeeeeeee....eeeeeeee..eeeeeee......eee....eeeeee....eeeeee..hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1i7a D   3 EQPIFTTRAHVFQI------NWVPASKQAVTVSYFYDVTRNSYRIISVDGAKVIINSTITPNMTFTKTSQKFGQWADSRANTVFGLGFSSELQLTKFAEKFQEVREAARF 401
                                    12   |     -|       32        42        52        62        72        82        92       102       401
                                        16     23                                                                                     111|
                                                                                                                                       401

Chain E from PDB  Type:PROTEIN  Length:3
                                   
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 1i7a E 201 FAF 203

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

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1I7A)

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (HOME2_MOUSE | Q9QWW1)
molecular function
    GO:0035256    G-protein coupled glutamate receptor binding    Interacting selectively and non-covalently with a G-protein coupled glutamate receptor (a metabotropic glutamate receptor).
    GO:0030160    GKAP/Homer scaffold activity    Functions as a physical support bridging the N-methyl-D-aspartate receptor-PSD-95-GKAP complex and the mGluR-Homer complex, which are involved in receptor signaling in synapses.
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    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).
biological process
    GO:0007216    G-protein coupled glutamate receptor signaling pathway    A series of molecular signals initiated by glutamate binding to a glutamate receptor on the surface of the target cell, and proceeding with the activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. Ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0048148    behavioral response to cocaine    Any process that results in a change in the behavior of an organism as a result of a cocaine stimulus.
    GO:0035584    calcium-mediated signaling using intracellular calcium source    A series of molecular signals in which a cell uses calcium ions released from an intracellular store to convert a signal into a response.
    GO:0048875    chemical homeostasis within a tissue    Any process involved in the maintenance of the internal steady state of the amount of a chemical at the level of the tissue.
    GO:0008277    regulation of G-protein coupled receptor protein signaling pathway    Any process that modulates the frequency, rate or extent of G-protein coupled receptor protein signaling pathway activity.
    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: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:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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.
    GO:0014069    postsynaptic density of dendrite    An electron dense network of proteins within and adjacent to the postsynaptic membrane of the dendrite of asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components.
    GO:0045211    postsynaptic membrane    A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane.
    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:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.

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 Related Entries

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

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(-) Related Entries Specified in the PDB File

1ddv 1DDV IS HOMER 1B FROM RAT WITH BOUND MGLUR PEPTIDE
1ddw 1DDW IS HOMER 1B FROM RAT