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(-) Description

Title :  CRYSTAL STRUCTURE OF AN INTEGRIN-BINDING FRAGMENT OF VASCULAR CELL ADHESION MOLECULE-1 AT 1.8 ANGSTROMS RESOLUTION
 
Authors :  E. Y. Jones, K. Harlos, M. J. Bottomley, R. C. Robinson, P. C. Driscoll, R. M. Edwards, J. M. Clements, T. J. Dudgeon, D. I. Stuart
Date :  21 Mar 95  (Deposition) - 15 Sep 95  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Immunoglobulin Superfamily, Integrin-Binding, Cell Adhesion Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Y. Jones, K. Harlos, M. J. Bottomley, R. C. Robinson, P. C. Driscoll, R. M. Edwards, J. M. Clements, T. J. Dudgeon, D. I. Stuart
Crystal Structure Of An Integrin-Binding Fragment Of Vascular Cell Adhesion Molecule-1 At 1. 8 A Resolution.
Nature V. 373 539 1995
PubMed-ID: 7531291  |  Reference-DOI: 10.1038/373539A0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HUMAN VASCULAR CELL ADHESION MOLECULE-1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    StrainHW1110
    SynonymVCAM-D1,2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1VCA)

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:23 -A:71
2A:28 -A:75
3A:113 -A:171
4B:23 -B:71
5B:28 -B:75
6B:113 -B:171

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Thr A:6 -Pro A:7
2Asn A:59 -Pro A:60
3Tyr A:119 -Pro A:120
4Thr B:6 -Pro B:7
5Asn B:59 -Pro B:60
6Tyr B:119 -Pro B:120

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (3, 6)

Asymmetric Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000002947281cENSE00001825682chr1:101185316-101185480165VCAM1_HUMAN1-22220--
1.2bENST000002947282bENSE00001067757chr1:101186032-101186307276VCAM1_HUMAN22-114932A:1-90
B:1-90
90
90
1.3ENST000002947283ENSE00001067755chr1:101188576-101188896321VCAM1_HUMAN114-2211082A:90-197
B:90-197
108
108
1.4ENST000002947284ENSE00001067758chr1:101190180-101190446267VCAM1_HUMAN221-310902A:197-199
B:197-199
3
3
1.5ENST000002947285ENSE00001067756chr1:101194663-101194938276VCAM1_HUMAN310-402930--
1.6ENST000002947286ENSE00001067753chr1:101196754-101197074321VCAM1_HUMAN402-5091080--
1.7ENST000002947287ENSE00001067759chr1:101197974-101198240267VCAM1_HUMAN509-598900--
1.8ENST000002947288ENSE00001067751chr1:101200058-101200324267VCAM1_HUMAN598-687900--
1.9cENST000002947289cENSE00001167778chr1:101203679-101204601923VCAM1_HUMAN687-739530--

(-) 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:199
 aligned with VCAM1_HUMAN | P19320 from UniProtKB/Swiss-Prot  Length:739

    Alignment length:199
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214         
          VCAM1_HUMAN    25 FKIETTPESRYLAQIGDSVSLTCSTTGCESPFFSWRTQIDSPLNGKVTNEGTTSTLTMNPVSFGNEHSYLCTATCESRKLEKGIQVEIYSFPKDPEIHLSGPLEAGKPITVKCSVADVYPFDRLEIDLLKGDHLMKSQEFLEDADRKSLETKSLEVTFTPVIEDIGKVLVCRAKLHIDEMDSVPTVRQAVKELQVYISP 223
               SCOP domains d1vcaa2 A:1-90 Vascular cell adhesion molecule-1 (VCAM-1)                                 d1vcaa1 A:91-199 Vascular cell adhesion molecule-1 (VCAM-1)                                                   SCOP domains
               CATH domains 1vcaA01 A:1-89 Immunoglobulins                                                           1vcaA02 A:90-199 Immunoglobulins                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...eeeee....eeeeeeee.....eeeeee........eeeee..eeeeee....hhh..eeeeeeee..eeeeeeeeeeee......eeee........eeeeeeee.....hhheeeeeee..eeeeeee............eeeeeeee..hhh...eeeeeeee..........eeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: A:1-90 UniProt: 22-114 [INCOMPLETE]                                       ----------------------------------------------------------------------------------------------------------1.4 Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------Exon 1.3  PDB: A:90-197 UniProt: 114-221                                                                    -- Transcript 1 (2)
                 1vca A   1 FKIETTPESRYLAQIGDSVSLTCSTTGCESPFFSWRTQIDSPLNGKVTNEGTTSTLTMNPVSFGNEHSYLCTATCESRKLEKGIQVEIYSFPKDPEIHLSGPLEAGKPITVKCSVADVYPFDRLEIDLLKGDHLMKSQEFLEDADRKSLETKSLEVTFTPVIEDIGKVLVCRAKLHIDEMDSVPTVRQAVKELQVYISP 199
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190         

Chain B from PDB  Type:PROTEIN  Length:199
 aligned with VCAM1_HUMAN | P19320 from UniProtKB/Swiss-Prot  Length:739

    Alignment length:199
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214         
          VCAM1_HUMAN    25 FKIETTPESRYLAQIGDSVSLTCSTTGCESPFFSWRTQIDSPLNGKVTNEGTTSTLTMNPVSFGNEHSYLCTATCESRKLEKGIQVEIYSFPKDPEIHLSGPLEAGKPITVKCSVADVYPFDRLEIDLLKGDHLMKSQEFLEDADRKSLETKSLEVTFTPVIEDIGKVLVCRAKLHIDEMDSVPTVRQAVKELQVYISP 223
               SCOP domains d1vcab2 B:1-90 Vascular cell adhesion molecule-1 (VCAM-1)                                 d1vcab1 B:91-199 Vascular cell adhesion molecule-1 (VCAM-1)                                                   SCOP domains
               CATH domains 1vcaB01 B:1-89 Immunoglobulins                                                           1vcaB02 B:90-199 Immunoglobulins                                                                               CATH domains
           Pfam domains (1) I-set-1vcaB03 B:1-88                                                                    --------------------C2-set-1vcaB01 B:109-197                                                                 -- Pfam domains (1)
           Pfam domains (2) I-set-1vcaB04 B:1-88                                                                    --------------------C2-set-1vcaB02 B:109-197                                                                 -- Pfam domains (2)
         Sec.struct. author .eeeee...eeeee....eeeeeeee.....eeeeee........eeeee..eeeeee....hhh..eeeeeeee..eeeeeeeeeeee......eeee........eeeeeeee.....hhheeeeeee..eeeeeee............eeeeeeee..hhh...eeeeeeee..........eeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: B:1-90 UniProt: 22-114 [INCOMPLETE]                                       ----------------------------------------------------------------------------------------------------------1.4 Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------Exon 1.3  PDB: B:90-197 UniProt: 114-221                                                                    -- Transcript 1 (2)
                 1vca B   1 FKIETTPESRYLAQIGDSVSLTCSTTGCESPFFSWRTQIDSPLNGKVTNEGTTSTLTMNPVSFGNEHSYLCTATCESRKLEKGIQVEIYSFPKDPEIHLSGPLEAGKPITVKCSVADVYPFDRLEIDLLKGDHLMKSQEFLEDADRKSLETKSLEVTFTPVIEDIGKVLVCRAKLHIDEMDSVPTVRQAVKELQVYISP 199
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190         

   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  (2, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: Ig (577)

(-) Gene Ontology  (48, 48)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (VCAM1_HUMAN | P19320)
molecular function
    GO:0050839    cell adhesion molecule binding    Interacting selectively and non-covalently with a cell adhesion molecule.
    GO:0005178    integrin binding    Interacting selectively and non-covalently with an integrin.
    GO:0008131    primary amine oxidase activity    Catalysis of the reaction: a primary amine + H2O + O2 = an aldehyde + NH3 + hydrogen peroxide.
biological process
    GO:0030183    B cell differentiation    The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
    GO:0002526    acute inflammatory response    Inflammation which comprises a rapid, short-lived, relatively uniform response to acute injury or antigenic challenge and is characterized by accumulations of fluid, plasma proteins, and granulocytic leukocytes. An acute inflammatory response occurs within a matter of minutes or hours, and either resolves within a few days or becomes a chronic inflammatory response.
    GO:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0009308    amine metabolic process    The chemical reactions and pathways involving any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom.
    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: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: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:0007160    cell-matrix adhesion    The binding of a cell to the extracellular matrix via adhesion molecules.
    GO:0071356    cellular response to tumor necrosis factor    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 tumor necrosis factor stimulus.
    GO:0035924    cellular response to vascular endothelial 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 vascular endothelial growth factor stimulus.
    GO:0002544    chronic inflammatory response    Inflammation of prolonged duration (weeks or months) in which active inflammation, tissue destruction, and attempts at repair are proceeding simultaneously. Although it may follow acute inflammation, chronic inflammation frequently begins insidiously, as a low-grade, smoldering, often asymptomatic response.
    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:0060333    interferon-gamma-mediated signaling pathway    A series of molecular signals initiated by the binding of interferon-gamma to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Interferon gamma is the only member of the type II interferon found so far.
    GO:0007159    leukocyte cell-cell adhesion    The attachment of a leukocyte to another cell via adhesion molecules.
    GO:0050901    leukocyte tethering or rolling    Transient adhesive interactions between leukocytes and endothelial cells lining blood vessels. Carbohydrates on circulating leukocytes bind selectins on the vessel wall causing the leukocytes to slow down and roll along the inner surface of the vessel wall. During this rolling motion, transitory bonds are formed and broken between selectins and their ligands. Typically the first step in cellular extravasation (the movement of leukocytes out of the circulatory system, towards the site of tissue damage or infection).
    GO:0022614    membrane to membrane docking    The initial attachment of a membrane to a target membrane, mediated by proteins protruding from the two membranes. Docking requires only that the membranes come close enough for the proteins to interact and adhere.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0042102    positive regulation of T cell proliferation    Any process that activates or increases the rate or extent of T cell proliferation.
    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:0045471    response to ethanol    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 ethanol stimulus.
    GO:0001666    response to hypoxia    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 lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0010212    response to ionizing radiation    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 ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0035094    response to nicotine    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 nicotine 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:0010043    response to zinc 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 zinc ion stimulus.
    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.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0071065    alpha9-beta1 integrin-vascular cell adhesion molecule-1 complex    A protein complex that consists of an alpha9-beta1 integrin complex bound to vascular cell adhesion molecule-1.
    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:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005769    early endosome    A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    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: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: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: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: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: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:0002102    podosome    An actin-rich adhesion structure characterized by formation upon cell substrate contact and localization at the substrate-attached part of the cell, contain an F-actin-rich core surrounded by a ring structure containing proteins such as vinculin and talin, and have a diameter of 0.5 mm.
    GO:0042383    sarcolemma    The outer membrane of a muscle cell, consisting of the plasma membrane, a covering basement membrane (about 100 nm thick and sometimes common to more than one fiber), and the associated loose network of collagen fibers.

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 Related Entries

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

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        VCAM1_HUMAN | P193201ij9 1vsc

(-) Related Entries Specified in the PDB File

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