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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN MYELOID CELL ACTIVATING RECEPTOR TREM-1
 
Authors :  S. Radaev, M. Kattah, B. Rostro, M. Colonna, P. D. Sun
Date :  21 Aug 03  (Deposition) - 09 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  V-Type Ig-Like Domain, Immunoglobulin-Like, Immune System Receptor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Radaev, M. Kattah, B. Rostro, M. Colonna, P. D. Sun
Crystal Structure Of The Human Myeloid Cell Activating Receptor Trem-1
Structure V. 11 1527 2003
PubMed-ID: 14656437  |  Reference-DOI: 10.1016/J.STR.2003.11.001
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRIGGERING RECEPTOR EXPRESSED ON MYELOID CELLS 1
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-22B
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentEXTRACELLULAR DOMAIN
    GeneTREM1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1GSH1Ligand/IonGLUTATHIONE
2SO410Ligand/IonSULFATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1GSH1Ligand/IonGLUTATHIONE
2SO45Ligand/IonSULFATE ION
Biological Unit 2 (1, 5)
No.NameCountTypeFull Name
1GSH-1Ligand/IonGLUTATHIONE
2SO45Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:28 , ARG A:130 , LYS B:120BINDING SITE FOR RESIDUE SO4 A 400
02AC2SOFTWARELYS B:120 , HOH B:1406BINDING SITE FOR RESIDUE SO4 B 500
03AC3SOFTWAREARG A:84BINDING SITE FOR RESIDUE SO4 A 600
04AC4SOFTWARELYS A:23 , LYS B:47BINDING SITE FOR RESIDUE SO4 A 700
05AC5SOFTWARELYS A:120 , LYS B:28 , ARG B:130BINDING SITE FOR RESIDUE SO4 B 1400
06AC6SOFTWARELYS C:28 , ARG C:130 , HOH C:2625 , LYS D:120BINDING SITE FOR RESIDUE SO4 C 2400
07AC7SOFTWARELYS D:120 , HOH D:3705BINDING SITE FOR RESIDUE SO4 D 2500
08AC8SOFTWAREARG C:84BINDING SITE FOR RESIDUE SO4 C 2600
09AC9SOFTWARELYS C:120 , LYS D:28 , ARG D:130BINDING SITE FOR RESIDUE SO4 D 3400
10BC1SOFTWAREARG D:59 , LYS D:65BINDING SITE FOR RESIDUE SO4 D 3700
11BC2SOFTWAREGLN A:52 , THR A:66 , CYS A:69 , TYR A:116 , ASP B:60BINDING SITE FOR RESIDUE GSH A 999

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:41 -A:113
2B:41 -B:113
3C:41 -C:113
4D:41 -D:113

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Arg A:72 -Pro A:73
2Arg B:72 -Pro B:73
3Arg C:72 -Pro C:73
4Arg D:72 -Pro D:73

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 12)

Asymmetric Unit (3, 12)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_019333T25STREM1_HUMANPolymorphism2234237A/B/C/DT25S
2UniProtVAR_035525R97STREM1_HUMANUnclassified  ---A/B/C/DR97S
3UniProtVAR_049949K135TTREM1_HUMANPolymorphism34727391A/B/C/DL135T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_019333T25STREM1_HUMANPolymorphism2234237A/BT25S
2UniProtVAR_035525R97STREM1_HUMANUnclassified  ---A/BR97S
3UniProtVAR_049949K135TTREM1_HUMANPolymorphism34727391A/BL135T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_019333T25STREM1_HUMANPolymorphism2234237C/DT25S
2UniProtVAR_035525R97STREM1_HUMANUnclassified  ---C/DR97S
3UniProtVAR_049949K135TTREM1_HUMANPolymorphism34727391C/DL135T

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Q8M)

(-) Exons   (3, 12)

Asymmetric Unit (3, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002447091ENSE00001338886chr6:41254457-41254345113TREM1_HUMAN1-17174A:16-17
B:16-17
C:16-17
D:16-17
2
2
2
2
1.2ENST000002447092ENSE00000849881chr6:41250489-41250133357TREM1_HUMAN17-1361204A:17-136
B:17-136
C:17-136
D:17-136
120
120
120
120
1.3ENST000002447093ENSE00000750662chr6:41248891-41248699193TREM1_HUMAN136-200654A:136-136
B:136-136
C:136-136
D:136-136
1
1
1
1
1.4ENST000002447094ENSE00002148464chr6:41243968-41243712257TREM1_HUMAN200-234350--

(-) 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:121
 aligned with TREM1_HUMAN | Q9NP99 from UniProtKB/Swiss-Prot  Length:234

    Alignment length:121
                                    25        35        45        55        65        75        85        95       105       115       125       135 
          TREM1_HUMAN    16 SELRAATKLTEEKYELKEGQTLDVKCDYTLEKFASSQKAWQIIRDGEMPKTLACTERPSKNSHPVQVGRIILEDYHDHGLLRVRMVNLQVEDSGLYQCVIYQPPKEPHMLFDRIRLVVTKG 136
               SCOP domains d1q8ma_ A: TREM-1 (triggering receptor expressed on myeloid cells 1)                                                      SCOP domains
               CATH domains 1q8mA00 A:16-136 Immunoglobulins                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...eee.eeeeeee....eeeeee..hhhhh...eeeeeee...eeeeeee..........eee..eeeeee....eeeeee...hhhhheeeeeee.......eee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------S-----------------------------------------------------------------------S-------------------------------------T- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.----------------------------------------------------------------------------------------------------------------------1 Transcript 1 (1)
           Transcript 1 (2) -Exon 1.2  PDB: A:17-136 UniProt: 17-136                                                                                  Transcript 1 (2)
                 1q8m A  16 MELRAATKLTEEKYELKEGQTLDVKCDYTLEKFASSQKAWQIIRDGEMPKTLACTERPSKNSHPVQVGRIILEDYHDHGLLRVRMVNLQVEDSGLYQCVIYQPPKEPHMLFDRIRLVVTLE 136
                                    25        35        45        55        65        75        85        95       105       115       125       135 

Chain B from PDB  Type:PROTEIN  Length:121
 aligned with TREM1_HUMAN | Q9NP99 from UniProtKB/Swiss-Prot  Length:234

    Alignment length:121
                                    25        35        45        55        65        75        85        95       105       115       125       135 
          TREM1_HUMAN    16 SELRAATKLTEEKYELKEGQTLDVKCDYTLEKFASSQKAWQIIRDGEMPKTLACTERPSKNSHPVQVGRIILEDYHDHGLLRVRMVNLQVEDSGLYQCVIYQPPKEPHMLFDRIRLVVTKG 136
               SCOP domains d1q8mb_ B: TREM-1 (triggering receptor expressed on myeloid cells 1)                                                      SCOP domains
               CATH domains 1q8mB00 B:16-136 Immunoglobulins                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..eee.eeeeeee....eeeee...hhhhh...eeeeeee...eeeeeee..........eee..eeeeeehhhheeeeee...hhhhheeeeeee.......eee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------S-----------------------------------------------------------------------S-------------------------------------T- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.----------------------------------------------------------------------------------------------------------------------1 Transcript 1 (1)
           Transcript 1 (2) -Exon 1.2  PDB: B:17-136 UniProt: 17-136                                                                                  Transcript 1 (2)
                 1q8m B  16 MELRAATKLTEEKYELKEGQTLDVKCDYTLEKFASSQKAWQIIRDGEMPKTLACTERPSKNSHPVQVGRIILEDYHDHGLLRVRMVNLQVEDSGLYQCVIYQPPKEPHMLFDRIRLVVTLE 136
                                    25        35        45        55        65        75        85        95       105       115       125       135 

Chain C from PDB  Type:PROTEIN  Length:121
 aligned with TREM1_HUMAN | Q9NP99 from UniProtKB/Swiss-Prot  Length:234

    Alignment length:121
                                    25        35        45        55        65        75        85        95       105       115       125       135 
          TREM1_HUMAN    16 SELRAATKLTEEKYELKEGQTLDVKCDYTLEKFASSQKAWQIIRDGEMPKTLACTERPSKNSHPVQVGRIILEDYHDHGLLRVRMVNLQVEDSGLYQCVIYQPPKEPHMLFDRIRLVVTKG 136
               SCOP domains d1q8mc_ C: TREM-1 (triggering receptor expressed on myeloid cells 1)                                                      SCOP domains
               CATH domains 1q8mC00 C:16-136 Immunoglobulins                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..eee.eeeeeee....eeeeee..hhhhh...eeeeeee...eeeeeee..........eee..eeeeee....eeeeee...hhhhheeeeeee.......eeee.eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------S-----------------------------------------------------------------------S-------------------------------------T- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.----------------------------------------------------------------------------------------------------------------------1 Transcript 1 (1)
           Transcript 1 (2) -Exon 1.2  PDB: C:17-136 UniProt: 17-136                                                                                  Transcript 1 (2)
                 1q8m C  16 MELRAATKLTEEKYELKEGQTLDVKCDYTLEKFASSQKAWQIIRDGEMPKTLACTERPSKNSHPVQVGRIILEDYHDHGLLRVRMVNLQVEDSGLYQCVIYQPPKEPHMLFDRIRLVVTLE 136
                                    25        35        45        55        65        75        85        95       105       115       125       135 

Chain D from PDB  Type:PROTEIN  Length:121
 aligned with TREM1_HUMAN | Q9NP99 from UniProtKB/Swiss-Prot  Length:234

    Alignment length:121
                                    25        35        45        55        65        75        85        95       105       115       125       135 
          TREM1_HUMAN    16 SELRAATKLTEEKYELKEGQTLDVKCDYTLEKFASSQKAWQIIRDGEMPKTLACTERPSKNSHPVQVGRIILEDYHDHGLLRVRMVNLQVEDSGLYQCVIYQPPKEPHMLFDRIRLVVTKG 136
               SCOP domains d1q8md_ D: TREM-1 (triggering receptor expressed on myeloid cells 1)                                                      SCOP domains
               CATH domains 1q8mD00 D:16-136 Immunoglobulins                                                                                          CATH domains
           Pfam domains (1) ----V-set-1q8mD01 D:20-133                                                                                            --- Pfam domains (1)
           Pfam domains (2) ----V-set-1q8mD02 D:20-133                                                                                            --- Pfam domains (2)
           Pfam domains (3) ----V-set-1q8mD03 D:20-133                                                                                            --- Pfam domains (3)
           Pfam domains (4) ----V-set-1q8mD04 D:20-133                                                                                            --- Pfam domains (4)
         Sec.struct. author .eeeeeeee.eeeeeee....eeeeee..hhhhh...eeeeeee...eeeeeee..........eee..eeeeee....eeeeee...hhhhheeeeeee.......eee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------S-----------------------------------------------------------------------S-------------------------------------T- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.----------------------------------------------------------------------------------------------------------------------1 Transcript 1 (1)
           Transcript 1 (2) -Exon 1.2  PDB: D:17-136 UniProt: 17-136                                                                                  Transcript 1 (2)
                 1q8m D  16 MELRAATKLTEEKYELKEGQTLDVKCDYTLEKFASSQKAWQIIRDGEMPKTLACTERPSKNSHPVQVGRIILEDYHDHGLLRVRMVNLQVEDSGLYQCVIYQPPKEPHMLFDRIRLVVTLE 136
                                    25        35        45        55        65        75        85        95       105       115       125       135 

   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  (1, 4)

Asymmetric Unit
(-)
Clan: Ig (577)
(-)
Family: V-set (144)
1aV-set-1q8mD01D:20-133
1bV-set-1q8mD02D:20-133
1cV-set-1q8mD03D:20-133
1dV-set-1q8mD04D:20-133

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (TREM1_HUMAN | Q9NP99)
molecular function
    GO:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
    GO:0097110    scaffold protein binding    Interacting selectively and non-covalently with a scaffold protein. Scaffold proteins are crucial regulators of many key signaling pathways. Although not strictly defined in function, they are known to interact and/or bind with multiple members of a signaling pathway, tethering them into complexes.
biological process
    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:0050755    chemokine metabolic process    The chemical reactions and pathways involving chemokines, any member of a family of small chemotactic cytokines; their name is derived from their ability to induce directed chemotaxis in nearby responsive cells. All chemokines possess a number of conserved cysteine residues involved in intramolecular disulfide bond formation. Some chemokines are considered pro-inflammatory and can be induced during an immune response to recruit cells of the immune system to a site of infection, while others are considered homeostatic and are involved in controlling the migration of cells during normal processes of tissue maintenance or development. Chemokines are found in all vertebrates, some viruses and some bacteria.
    GO:0042107    cytokine metabolic process    The chemical reactions and pathways involving cytokines, any of a group of proteins or glycoproteins that function to control the survival, growth and differentiation of tissues and cells, and which have autocrine and paracrine activity.
    GO:0002374    cytokine secretion involved in immune response    The regulated release of cytokines from a cell that contributes to an immune response.
    GO:0006959    humoral immune response    An immune response mediated through a body fluid.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    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:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    GO:0030593    neutrophil chemotaxis    The directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
    GO:0072672    neutrophil extravasation    The migration of a neutrophil from the blood vessels into the surrounding tissue.
    GO:0070945    neutrophil mediated killing of gram-negative bacterium    The directed killing of a gram-negative bacterium by a neutrophil.
    GO:0002230    positive regulation of defense response to virus by host    Any host process that results in the promotion of antiviral immune response mechanisms, thereby limiting viral replication.
    GO:0098779    positive regulation of macromitophagy in response to mitochondrial depolarization    The macromitophagy process that is triggered by a detection of the loss of mitochondrial membrane potential.
    GO:0050776    regulation of immune response    Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
    GO:0098792    xenophagy    The macroautophagy process in which a region of cytoplasm containing an intracellular pathogen or some part of an intracellular pathogen (e.g. viral capsid) is enclosed in a double membrane bound autophagosome, which then fuses with the lysosome leading to degradation of the contents.
cellular component
    GO:0005623    cell    The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
    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: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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    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.

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 Related Entries

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

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        TREM1_HUMAN | Q9NP991smo

(-) Related Entries Specified in the PDB File

1hkf 1i85 1tvd 3hfl