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(-) Description

Title :  NMR SOLUTION STRUCTURE OF THE INSERTED DOMAIN OF HUMAN LEUKOCYTE FUNCTION ASSOCIATED ANTIGEN-1
 
Authors :  G. B. Legge, R. W. Kriwacki, J. Chung, U. Hommel, P. Ramage, D. A. Case, H. P. E. Wright
Date :  24 Nov 99  (Deposition) - 03 Feb 00  (Release) - 12 Nov 14  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (22x)
NMR Structure *:  A  (1x)
Keywords :  Rossmann Fold, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. B. Legge, R. W. Kriwacki, J. Chung, U. Hommel, P. Ramage, D. A. Case, H. J. Dyson, P. E. Wright
Nmr Solution Structure Of The Inserted Domain Of Human Leukocyte Function Associated Antigen-1.
J. Mol. Biol. V. 295 1251 2000
PubMed-ID: 10653701  |  Reference-DOI: 10.1006/JMBI.1999.3409

(-) Compounds

Molecule 1 - LEUKOCYTE FUNCTION ASSOCIATED ANTIGEN-1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET17B
    Expression System Taxid562
    FragmentINSERTED DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
NMR Structure (22x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1DGQ)

(-) Sites  (0, 0)

(no "Site" information available for 1DGQ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 22)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22Lys A:280 -Pro A:281

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_025236R214WITAL_HUMANPolymorphism1064524AW189W

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
NMR Structure * (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_025236R214WITAL_HUMANPolymorphism1064524AW189W

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VWFAPS50234 VWFA domain profile.ITAL_HUMAN156-327  1A:131-302
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VWFAPS50234 VWFA domain profile.ITAL_HUMAN156-327  1A:131-302

(-) Exons   (6, 6)

NMR Structure (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003567981aENSE00002147085chr16:30483983-30484219237ITAL_HUMAN1-21210--
1.2bENST000003567982bENSE00001770886chr16:30485517-30485619103ITAL_HUMAN21-55350--
1.3ENST000003567983ENSE00001621476chr16:30486627-3048672195ITAL_HUMAN55-87330--
1.4ENST000003567984ENSE00001775052chr16:30486834-3048690168ITAL_HUMAN87-109231A:124-1263
1.5ENST000003567985ENSE00001718084chr16:30490412-30490529118ITAL_HUMAN110-149400--
1.6ENST000003567986ENSE00001643987chr16:30490652-30490782131ITAL_HUMAN149-192441A:127-16741
1.7ENST000003567987ENSE00001594214chr16:30492760-30492905146ITAL_HUMAN193-241491A:168-21649
1.8ENST000003567988ENSE00001756914chr16:30495148-30495280133ITAL_HUMAN241-285451A:216-26045
1.9ENST000003567989ENSE00001781646chr16:30495434-30495584151ITAL_HUMAN286-336511A:261-31151
1.10ENST0000035679810ENSE00001704215chr16:30500403-3050047674ITAL_HUMAN336-360251A:311-3111
1.11ENST0000035679811ENSE00001741327chr16:30500575-30500707133ITAL_HUMAN361-405450--
1.12ENST0000035679812ENSE00001592674chr16:30505533-30505684152ITAL_HUMAN405-455510--
1.13ENST0000035679813ENSE00001785598chr16:30506034-30506171138ITAL_HUMAN456-501460--
1.14ENST0000035679814ENSE00001694693chr16:30507418-30507615198ITAL_HUMAN502-567660--
1.15ENST0000035679815ENSE00001704204chr16:30507757-30507887131ITAL_HUMAN568-611440--
1.16aENST0000035679816aENSE00001611961chr16:30510395-30510555161ITAL_HUMAN611-665550--
1.17ENST0000035679817ENSE00001610939chr16:30510659-30510810152ITAL_HUMAN665-715510--
1.18ENST0000035679818ENSE00001693046chr16:30515496-3051558590ITAL_HUMAN716-745300--
1.19aENST0000035679819aENSE00001609957chr16:30516565-3051662157ITAL_HUMAN746-764190--
1.20ENST0000035679820ENSE00001755479chr16:30516710-3051678374ITAL_HUMAN765-789250--
1.21ENST0000035679821ENSE00001735592chr16:30518036-30518177142ITAL_HUMAN789-836480--
1.22ENST0000035679822ENSE00001788360chr16:30521682-30521792111ITAL_HUMAN837-873370--
1.23aENST0000035679823aENSE00001758712chr16:30522202-3052228180ITAL_HUMAN874-900270--
1.24ENST0000035679824ENSE00001615572chr16:30522371-3052245787ITAL_HUMAN900-929300--
1.25ENST0000035679825ENSE00001670842chr16:30525092-3052516776ITAL_HUMAN929-954260--
1.26ENST0000035679826ENSE00001795073chr16:30528294-30528407114ITAL_HUMAN955-992380--
1.27ENST0000035679827ENSE00001688272chr16:30528970-3052902657ITAL_HUMAN993-1011190--
1.28ENST0000035679828ENSE00001734661chr16:30529118-3052921699ITAL_HUMAN1012-1044330--
1.29ENST0000035679829ENSE00001721322chr16:30529945-3053004096ITAL_HUMAN1045-1076320--
1.30ENST0000035679830ENSE00001673761chr16:30531178-30531288111ITAL_HUMAN1077-1113370--
1.31bENST0000035679831bENSE00001399855chr16:30532813-305345051693ITAL_HUMAN1114-1170570--

(-) Sequences/Alignments

NMR Structure
   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:188
 aligned with ITAL_HUMAN | P20701 from UniProtKB/Swiss-Prot  Length:1170

    Alignment length:238
                                   108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328        
           ITAL_HUMAN    99 LATDPTDGSILACDPGLSRTCDQNTYLSGLCYLFRQNLQGPMLQGRPGFQECIKGNVDLVFLFDGSMSLQPDEFQKILDFMKDVMKKLSNTSYQFAAVQFSTSYKTEFDFSDYVKRKDPDALLKHVKHMLLLTNTFGAINYVATEVFREELGARPDATKVLIIITDGEATDSGNIDAAKDIIRYIIGIGKHFQTKESQETLHKFASKPASEFVKILDTFEKLKDLFTELQKKIYVIEG 336
               SCOP domains d1d                                                  gqa_ A: Integrin CD11a/CD18 (Leukocyte function associated antigen-1, LFA-1)                                                                                                              SCOP domains
               CATH domains 1dg                                                  qA00 A:124-311  [code=3.40.50.410, no name defined]                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...--------------------------------------------------...eeeeeeee.....hhhhhhhhhhhhhhhhhhh....eeeeeeee...eeeeehhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh..hhhhh.....eeeeeeee.........hhhhh..eeeeeee.....hhhhhhhhhhhh..hhhhheeee.hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------W-------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------VWFA  PDB: A:131-302 UniProt: 156-327                                                                                                                                       --------- PROSITE
           Transcript 1 (1) Exon 1.4   Exon 1.5  PDB: - UniProt: 110-149       -------------------------------------------Exon 1.7  PDB: A:168-216 UniProt: 193-241        ----------------------------------------------------------------------------------------------1 Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------Exon 1.6  PDB: A:127-167 UniProt: 149-192   ------------------------------------------------Exon 1.8  PDB: A:216-260 UniProt: 241-285    Exon 1.9  PDB: A:261-311 UniProt: 286-336           Transcript 1 (2)
                 1dgq A 124 MAS--------------------------------------------------KGNVDLVFLFDGSMSLQPDEFQKILDFMKDVMKKLSNTSYQFAAVQFSTSYKTEFDFSDYVKWKDPDALLKHVKHMLLLTNTFGAINYVATEVFREELGARPDATKVLIIITDGEATDSGNIDAAKDIIRYIIGIGKHFQTKESQETLHKFASKPASEFVKILDTFEKLKDLFTELQKKIYVIEG 311
                              |      -         -         -         -         -   |   133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303        
                              |                                                127                                                                                                                                                                                        
                            126                                                                                                                                                                                                                                           

   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)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (27, 27)

NMR Structure(hide GO term definitions)
Chain A   (ITAL_HUMAN | P20701)
molecular function
    GO:0030369    ICAM-3 receptor activity    Combining with ICAM-3, intercellular adhesion molecule 3, and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity. ICAM-3, or CD50, are constitutively expressed on monocytes, granulocytes and lymphocytes; on physiological stimulation, they become transiently phosphorylated on serine residues.
    GO:0050839    cell adhesion molecule binding    Interacting selectively and non-covalently with a cell adhesion molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
    GO:0002291    T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell    The change in morphology and behavior of a mature or immature T cell resulting from exposure to an antigen for which its T cell receptor is specific bound to an MHC molecule on an antigen presenting cell, leading to the initiation or perpetuation of an immune response.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0007160    cell-matrix adhesion    The binding of a cell to the extracellular matrix via adhesion molecules.
    GO:0030198    extracellular matrix organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
    GO:0007157    heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules    The attachment of an adhesion molecule in one cell to a nonidentical adhesion molecule in an adjacent cell.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0007229    integrin-mediated signaling pathway    A series of molecular signals initiated by the binding of extracellular ligand to an integrin on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0007159    leukocyte cell-cell adhesion    The attachment of a leukocyte to another cell via adhesion molecules.
    GO:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    GO:0006928    movement of cell or subcellular component    The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore.
    GO:0043113    receptor clustering    The receptor metabolic process that results in grouping of a set of receptors at a cellular location, often to amplify the sensitivity of a signaling response.
    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: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:0016337    single organismal cell-cell adhesion    The attachment of one cell to another cell via adhesion molecules, where both cells are part of the same organism.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    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: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:0034687    integrin alphaL-beta2 complex    An integrin complex that comprises one alphaL subunit and one beta2 subunit.
    GO:0008305    integrin complex    A protein complex that is composed of one alpha subunit and one beta subunit, both of which are members of the integrin superfamily of cell adhesion receptors; the complex spans the plasma membrane and binds to extracellular matrix ligands, cell-surface ligands, and soluble ligands.
    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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    Lys A:280 - Pro A:281   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        ITAL_HUMAN | P207011cqp 1ij4 1lfa 1mjn 1mq8 1mq9 1mqa 1rd4 1t0p 1xdd 1xdg 1xuo 1zon 1zoo 1zop 2ica 2k8o 2m3e 2o7n 3bn3 3bqm 3bqn 3e2m 3eoa 3eob 3f74 3f78 3hi6 3m6f 3tcx 4ixd 5e6r 5e6s 5e6u

(-) Related Entries Specified in the PDB File

1lfa I-DOMAIN FRAGMENT OF LFA-1 WITH BOUND MN2+ X-RAY DIFFRACTION RESOLUTION: 1.8 A
1zon I-DOMAIN FRAGMENT OF LFA-1 WITH BOUND MG2+ X-RAY DIFFRACTION, SINGLE CRYSTAL RESOLUTION: 2.00 A
1zoo I-DOMAIN FRAGMENT OF LFA-1 IN THE ABSENCE OF DIVALENT CATION X-RAY DIFFRACTION RESOLUTION: 3.00 A
1zop I-DOMAIN FRAGMENT OF LFA-1 WITH BOUND MN2+ X-RAY DIFFRACTION