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(-) Description

Title :  BONE MORPHOGENETIC PROTEIN-7
 
Authors :  D. L. Griffith, D. L. Scott
Date :  14 Dec 95  (Deposition) - 23 Jul 97  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Morphogen, Transforming Growth Factor, Cytokine, Bone, Cartilage, Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. L. Griffith, P. C. Keck, T. K. Sampath, D. C. Rueger, W. D. Carlson
Three-Dimensional Structure Of Recombinant Human Osteogenic Protein 1: Structural Paradigm For The Transforming Growth Factor Beta Superfamily.
Proc. Natl. Acad. Sci. Usa V. 93 878 1996
PubMed-ID: 8570652  |  Reference-DOI: 10.1073/PNAS.93.2.878
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BONE MORPHOGENETIC PROTEIN-7
    ChainsA
    EngineeredYES
    Expression SystemCRICETULUS GRISEUS
    Expression System CommonCHINESE HAMSTER
    Expression System GeneHOP-1 CDNA
    Expression System Taxid10029
    GeneHOP-1 CDNA
    OrganOVARY
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsREFERENCE, T.K. SAMPATH, ET AL. (1992) J. BIOL. CHEM. 267, 20452-20362
    SynonymOSTEOGENIC PROTEIN-1, HOP-1, BMP-7

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1BMP)

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:38 -A:104
2A:67 -A:136
3A:71 -A:138
4A:103 -A:103

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:58 -Pro A:59
2Phe A:73 -Pro A:74

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TGF_BETA_1PS00250 TGF-beta family signature.BMP7_HUMAN348-363  1A:56-71
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TGF_BETA_1PS00250 TGF-beta family signature.BMP7_HUMAN348-363  2A:56-71

(-) Exons   (3, 3)

Asymmetric Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003958631bENSE00001908937chr20:55841684-55840761924BMP7_HUMAN1-1401400--
1.3ENST000003958633ENSE00000662923chr20:55803477-55803285193BMP7_HUMAN140-204650--
1.7aENST000003958637aENSE00000662922chr20:55777679-55777531149BMP7_HUMAN204-254510--
1.9ENST000003958639ENSE00000662921chr20:55758975-55758778198BMP7_HUMAN254-320670--
1.11ENST0000039586311ENSE00000662920chr20:55750063-5574998777BMP7_HUMAN320-345261A:36-5318
1.12cENST0000039586312cENSE00001710703chr20:55748366-55748256111BMP7_HUMAN346-382371A:54-9037
1.13eENST0000039586313eENSE00001523115chr20:55746164-557438042361BMP7_HUMAN383-431491A:91-13949

(-) 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:104
 aligned with BMP7_HUMAN | P18075 from UniProtKB/Swiss-Prot  Length:431

    Alignment length:104
                                   337       347       357       367       377       387       397       407       417       427    
           BMP7_HUMAN   328 QACKKHELYVSFRDLGWQDWIIAPEGYAAYYCEGECAFPLNSYMNATNHAIVQTLVHFINPETVPKPCCAPTQLNAISVLYFDDSSNVILKKYRNMVVRACGCH 431
               SCOP domains d1bmpa_ A: Bone morphogenetic protein-7 (BMP-7)                                                          SCOP domains
               CATH domains 1bmpA00 A:36-139 Cystine-knot cytokines                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..eee..............eee..eee...............hhhhhhhhhh.........eeeeee...eeeeee.....eeeeee......eeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------TGF_BETA_1      -------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.11         Exon 1.12c  PDB: A:54-90             Exon 1.13e  PDB: A:91-139 UniProt: 383-431        Transcript 1
                 1bmp A  36 QACKKHELYVSFRDLGWQDWIIAPEGYAAYYCEGECAFPLNSYMNATNHAIVQTLVHFINPETVPKPCCAPTQLNAISVLYFDDSSNVILKKYRNMVVRACGCH 139
                                    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, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (89, 89)

Asymmetric Unit(hide GO term definitions)
Chain A   (BMP7_HUMAN | P18075)
molecular function
    GO:0070700    BMP receptor binding    Interacting selectively and non-covalently with a BMP receptor.
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0008083    growth factor activity    The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    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:0005160    transforming growth factor beta receptor binding    Interacting selectively and non-covalently with the transforming growth factor beta receptor.
biological process
    GO:0030509    BMP signaling pathway    A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0060395    SMAD protein signal transduction    The cascade of processes by which a signal interacts with a receptor, causing a change in the activity of a SMAD protein, and ultimately effecting a change in the functioning of the cell.
    GO:0048646    anatomical structure formation involved in morphogenesis    The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
    GO:0009887    animal organ morphogenesis    Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    GO:0007411    axon guidance    The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
    GO:0060445    branching involved in salivary gland morphogenesis    The process in which the branching structure of the salivary gland is generated and organized.
    GO:0048754    branching morphogenesis of an epithelial tube    The process in which the anatomical structures of branches in an epithelial tube are generated and organized. A tube is a long hollow cylinder.
    GO:0048593    camera-type eye morphogenesis    The process in which the anatomical structures of the eye are generated and organized. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field.
    GO:0051216    cartilage development    The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
    GO:0048468    cell development    The process whose specific outcome is the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0071773    cellular response to BMP 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 bone morphogenetic protein (BMP) stimulus.
    GO:0071456    cellular response to hypoxia    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 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:0016358    dendrite development    The process whose specific outcome is the progression of the dendrite over time, from its formation to the mature structure. A dendrite is a freely branching protoplasmic process of a nerve cell.
    GO:0048596    embryonic camera-type eye morphogenesis    The process in which the anatomical structures of the eye are generated and organized during embryonic development.
    GO:0030326    embryonic limb morphogenesis    The process, occurring in the embryo, by which the anatomical structures of the limb are generated and organized. A limb is an appendage of an animal used for locomotion or grasping.
    GO:0009880    embryonic pattern specification    The process that results in the patterns of cell differentiation that will arise in an embryo.
    GO:0060272    embryonic skeletal joint morphogenesis    The process in which the anatomical structures of skeletal joints are generated and organized during the embryonic phase. A skeletal joint is the connecting structure between the bones of the skeleton.
    GO:0030855    epithelial cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium.
    GO:0001837    epithelial to mesenchymal transition    A transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell.
    GO:0001654    eye development    The process whose specific outcome is the progression of the eye over time, from its formation to the mature structure. The eye is the organ of sight.
    GO:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    GO:0001822    kidney development    The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine.
    GO:0048762    mesenchymal cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a mesenchymal cell. A mesenchymal cell is a loosely associated cell that is part of the connective tissue in an organism. Mesenchymal cells give rise to more mature connective tissue cell types.
    GO:0060485    mesenchyme development    The process whose specific outcome is the progression of a mesenchymal tissue over time, from its formation to the mature structure. A mesenchymal tissue is made up of loosely packed stellate cells.
    GO:0001707    mesoderm formation    The process that gives rise to the mesoderm. This process pertains to the initial formation of the structure from unspecified parts.
    GO:0001823    mesonephros development    The process whose specific outcome is the progression of the mesonephros over time, from its formation to the mature structure. In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the mesonephros will form the mature kidney.
    GO:0072136    metanephric mesenchymal cell proliferation involved in metanephros development    The multiplication or reproduction of cells, resulting in the expansion of a metanephric mesenchymal cell population.
    GO:0072133    metanephric mesenchyme morphogenesis    The process in which the anatomical structures of a metanephric mesenchymal tissue are generated and organized. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros.
    GO:0001656    metanephros development    The process whose specific outcome is the progression of the metanephros over time, from its formation to the mature structure. In mammals, the metanephros is the excretory organ of the fetus, which develops into the mature kidney and is formed from the rear portion of the nephrogenic cord. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine.
    GO:0070487    monocyte aggregation    The adhesion of one monocyte to one or more other monocytes via adhesion molecules.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0043407    negative regulation of MAP kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of MAP kinase activity.
    GO:0042347    negative regulation of NF-kappaB import into nucleus    Any process that stops, prevents, or reduces the frequency, rate or extent of the transfer of NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters, from the cytoplasm into the nucleus, across the nuclear membrane.
    GO:0032088    negative regulation of NF-kappaB transcription factor activity    Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB.
    GO:0045746    negative regulation of Notch signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of the Notch signaling pathway.
    GO:0045786    negative regulation of cell cycle    Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle.
    GO:0060548    negative regulation of cell death    Any process that decreases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0072125    negative regulation of glomerular mesangial cell proliferation    Any process that decreases the frequency, rate or extent of glomerular mesangial cell proliferation.
    GO:0072040    negative regulation of mesenchymal cell apoptotic process involved in nephron morphogenesis    Any process that reduces the occurrence or rate of mesenchymal stem cell death by apoptotic process that contributes to the shaping of the nephron.
    GO:0045839    negative regulation of mitotic nuclear division    Any process that stops, prevents or reduces the rate or extent of mitosis. Mitosis is the division of the eukaryotic cell nucleus to produce two daughter nuclei that, usually, contain the identical chromosome complement to their mother.
    GO:0050768    negative regulation of neurogenesis    Any process that stops, prevents, or reduces the frequency, rate or extent of neurogenesis, the origin and formation of neurons.
    GO:0045665    negative regulation of neuron differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of neuron differentiation.
    GO:0042326    negative regulation of phosphorylation    Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule.
    GO:0060686    negative regulation of prostatic bud formation    Any process that decreases the rate, frequency, or extent of prostatic bud formation, the morphogenetic process in which a region of the fetal urogenital sinus epithelium is specified to become the prostate, resulting in prostate bud outgrowth.
    GO:0010664    negative regulation of striated muscle cell apoptotic process    Any process that decreases the rate or extent of striated muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a striated muscle cell and result in its death.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0072134    nephrogenic mesenchyme morphogenesis    The process in which the anatomical structures of a nephrogenic mesenchymal tissue are generated and organized. Nephrogenic mesenchyme is the tissue made up of loosely connected mesenchymal cells in the nephron.
    GO:0048812    neuron projection morphogenesis    The process in which the anatomical structures of a neuron projection are generated and organized. A neuron projection is any process extending from a neural cell, such as axons or dendrites.
    GO:0042475    odontogenesis of dentin-containing tooth    The process whose specific outcome is the progression of a dentin-containing tooth over time, from its formation to the mature structure. A dentin-containing tooth is a hard, bony organ borne on the jaw or other bone of a vertebrate, and is composed mainly of dentin, a dense calcified substance, covered by a layer of enamel.
    GO:0001503    ossification    The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
    GO:0007389    pattern specification process    Any developmental process that results in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0030501    positive regulation of bone mineralization    Any process that activates or increases the frequency, rate or extent of bone mineralization.
    GO:0010942    positive regulation of cell death    Any process that increases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
    GO:0045597    positive regulation of cell differentiation    Any process that activates or increases the frequency, rate or extent of cell differentiation.
    GO:1900006    positive regulation of dendrite development    Any process that activates or increases the frequency, rate or extent of dendrite development.
    GO:0034116    positive regulation of heterotypic cell-cell adhesion    Any process that activates or increases the frequency, rate, or extent of heterotypic cell-cell adhesion.
    GO:1900106    positive regulation of hyaluranon cable assembly    Any process that activates or increases the frequency, rate or extent of hyaluranon cable assembly.
    GO:0045666    positive regulation of neuron differentiation    Any process that activates or increases the frequency, rate or extent of neuron differentiation.
    GO:0045669    positive regulation of osteoblast differentiation    Any process that activates or increases the frequency, rate or extent of osteoblast differentiation.
    GO:0010862    positive regulation of pathway-restricted SMAD protein phosphorylation    Any process that increases the rate, frequency or extent of pathway-restricted SMAD protein phosphorylation. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways.
    GO:0010800    positive regulation of peptidyl-threonine phosphorylation    Any process that increases the frequency, rate or extent of peptidyl-threonine phosphorylation. Peptidyl-threonine phosphorylation is the phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0034504    protein localization to nucleus    A process in which a protein transports or maintains the localization of another protein to the nucleus.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0060687    regulation of branching involved in prostate gland morphogenesis    Any process that modulates the rate, frequency, or extent of prostate gland branching, the process in which the branching structure of the prostate gland is generated and organized. A branch is a division or offshoot from a main stem.
    GO:0060393    regulation of pathway-restricted SMAD protein phosphorylation    Any process that modulates the rate, frequency or extent of pathway-restricted SMAD protein phosphorylation. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways.
    GO:0042325    regulation of phosphorylation    Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule.
    GO:2000121    regulation of removal of superoxide radicals    Any process that modulates the frequency, rate or extent of removal of superoxide radicals.
    GO:0032355    response to estradiol    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 stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
    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:0033280    response to vitamin D    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 vitamin D stimulus.
    GO:0007435    salivary gland morphogenesis    The process in which the anatomical structures of the salivary gland are generated and organized.
    GO:0001501    skeletal system development    The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
    GO:0043401    steroid hormone mediated signaling pathway    A series of molecular signals mediated by a steroid hormone binding to a receptor.
    GO:0035239    tube morphogenesis    The process in which the anatomical structures of a tube are generated and organized. Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.
    GO:0001657    ureteric bud development    The process whose specific outcome is the progression of the ureteric bud over time, from its formation to the mature structure.
cellular component
    GO:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    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.

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

UniProtKB/Swiss-Prot
        BMP7_HUMAN | P180751lx5 1lxi 1m4u

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1BMP)