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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CYTOPLASMIC DOMAIN OF HUMAN PLEXIN B1
 
Authors :  Y. Tong, H. He, L. Shen, W. Tempel, F. Mackenzie, C. H. Arrowsmith, A. M. E C. Bountra, J. Weigelt, A. Bochkarev, H. Park, Structural Genomics Consortium (Sgc)
Date :  28 May 09  (Deposition) - 09 Jun 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  C,X
Keywords :  Structural Genomics Consortium, Sgc, Membrane, Transmembrane, Receptor, Cell Membrane, Glycoprotein, Phosphoprotein, Secreted, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Tong, P. K. Hota, J. Y. Penachioni, M. B. Hamaneh, S. Kim, R. S. Alviani, L. Shen, H. He, W. Tempel, L. Tamagnone, H. W. Park, M. Buc
Structure And Function Of The Intracellular Region Of The Plexin-B1 Transmembrane Receptor.
J. Biol. Chem. V. 284 35962 2009
PubMed-ID: 19843518  |  Reference-DOI: 10.1074/JBC.M109.056275

(-) Compounds

Molecule 1 - PLEXIN-B1
    ChainsX
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System StrainSF9
    Expression System Taxid7108
    FragmentCYTOPLASMIC DOMAIN (UNP RESIDUES 1511-2135)
    GenePLXNB1, KIAA0407, PLXN5, SEP
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSEMAPHORIN RECEPTOR SEP
 
Molecule 2 - UNKNOWN PEPTIDE
    ChainsC
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System StrainSF9
    Expression System Taxid7108
    GenePLXNB1, KIAA0407, PLXN5, SEP
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit CX

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 46)

Asymmetric/Biological Unit (2, 46)
No.NameCountTypeFull Name
1UNK27Mod. Amino Acid
2UNX19Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (0, 0)

(no "Site" information available for 3HM6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3HM6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3HM6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HM6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3HM6)

(-) Exons   (14, 14)

Asymmetric/Biological Unit (14, 14)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3bENST000003585363bENSE00001668057chr3:48470872-48470662211PLXB1_HUMAN-00--
1.4aENST000003585364aENSE00001428482chr3:48466742-4846669053PLXB1_HUMAN-00--
1.5aENST000003585365aENSE00001206107chr3:48466026-484649141113PLXB1_HUMAN1-3693690--
1.6ENST000003585366ENSE00001080883chr3:48464356-48464174183PLXB1_HUMAN370-430610--
1.7aENST000003585367aENSE00001080893chr3:48463868-48463740129PLXB1_HUMAN431-473430--
1.8ENST000003585368ENSE00001080898chr3:48463614-48463514101PLXB1_HUMAN474-507340--
1.9ENST000003585369ENSE00001080910chr3:48463215-48463083133PLXB1_HUMAN507-551450--
1.10ENST0000035853610ENSE00001080902chr3:48462793-48462637157PLXB1_HUMAN552-604530--
1.11ENST0000035853611ENSE00001080906chr3:48462365-48462257109PLXB1_HUMAN604-640370--
1.12ENST0000035853612ENSE00001080876chr3:48462182-48462074109PLXB1_HUMAN640-676370--
1.13cENST0000035853613cENSE00001326499chr3:48461666-48460986681PLXB1_HUMAN677-9032270--
1.13gENST0000035853613gENSE00001673675chr3:48460775-48460653123PLXB1_HUMAN904-944410--
1.14ENST0000035853614ENSE00001644091chr3:48460448-48460326123PLXB1_HUMAN945-985410--
1.15ENST0000035853615ENSE00001632794chr3:48459951-4845985894PLXB1_HUMAN986-1017320--
1.16bENST0000035853616bENSE00001689569chr3:48459772-48459600173PLXB1_HUMAN1017-1074580--
1.17ENST0000035853617ENSE00001688877chr3:48459471-48459320152PLXB1_HUMAN1075-1125510--
1.18bENST0000035853618bENSE00001630248chr3:48457860-48457755106PLXB1_HUMAN1125-1160360--
1.19ENST0000035853619ENSE00001685598chr3:48457576-48457440137PLXB1_HUMAN1161-1206460--
1.20aENST0000035853620aENSE00001604226chr3:48457168-48456992177PLXB1_HUMAN1206-1265600--
1.21cENST0000035853621cENSE00001725709chr3:48456756-48456585172PLXB1_HUMAN1265-1322580--
1.22bENST0000035853622bENSE00001726311chr3:48456450-48456208243PLXB1_HUMAN1323-1403810--
1.23cENST0000035853623cENSE00001731310chr3:48455480-48455304177PLXB1_HUMAN1404-1462590--
1.23hENST0000035853623hENSE00001788421chr3:48455227-48455079149PLXB1_HUMAN1463-1512500--
1.23jENST0000035853623jENSE00001633158chr3:48454578-48454478101PLXB1_HUMAN1512-1546350--
1.24aENST0000035853624aENSE00001749742chr3:48454368-48454151218PLXB1_HUMAN1546-1618731X:1563-1618 (gaps)56
1.25ENST0000035853625ENSE00001745479chr3:48454029-48453851179PLXB1_HUMAN1619-1678601X:1619-167860
1.26aENST0000035853626aENSE00001731741chr3:48453713-4845364767PLXB1_HUMAN1678-1700231X:1678-170023
1.26cENST0000035853626cENSE00001740702chr3:48453418-48453272147PLXB1_HUMAN1701-1749491X:1701-174949
1.27bENST0000035853627bENSE00001769186chr3:48452445-48452277169PLXB1_HUMAN1750-1806571X:1750-1806 (gaps)57
1.27dENST0000035853627dENSE00001752233chr3:48451967-48451864104PLXB1_HUMAN1806-1840351X:1806-184035
1.28aENST0000035853628aENSE00001597624chr3:48451789-4845170585PLXB1_HUMAN1841-1869291X:1841-185212
1.29bENST0000035853629bENSE00001747202chr3:48451486-48451314173PLXB1_HUMAN1869-1926581X:1879-1926 (gaps)48
1.30aENST0000035853630aENSE00001685743chr3:48451139-48450979161PLXB1_HUMAN1927-1980541X:1927-198054
1.30dENST0000035853630dENSE00001746046chr3:48450884-48450737148PLXB1_HUMAN1980-2029501X:1980-202445
1.31aENST0000035853631aENSE00001798246chr3:48448498-4844843465PLXB1_HUMAN2030-2051221X:2031-205121
1.32aENST0000035853632aENSE00001737780chr3:48448305-4844823076PLXB1_HUMAN2051-2076261X:2051-207626
1.33bENST0000035853633bENSE00001624889chr3:48447205-4844713175PLXB1_HUMAN2077-2101251X:2077-210125
1.34cENST0000035853634cENSE00001862726chr3:48445997-48445263735PLXB1_HUMAN2102-2135341X:2102-212928

(-) Sequences/Alignments

Asymmetric/Biological 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 C from PDB  Type:PROTEIN  Length:27
                                                            
               SCOP domains --------------------------- SCOP domains
               CATH domains --------------------------- CATH domains
               Pfam domains --------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------- SAPs(SNPs)
                    PROSITE --------------------------- PROSITE
                 Transcript --------------------------- Transcript
                3hm6 C 1007 xxxxxxxxxxxxxxxxxxxxxxxxxxx 1033
                            ||||||1016||||||1026|||||||
                         1007-UNK|1016-UNK|1025-UNK||||
                          1008-UNK|1017-UNK|1026-UNK|||
                           1009-UNK|1018-UNK|1027-UNK||
                            1010-UNK|1019-UNK|1028-UNK|
                             1011-UNK 1020-UNK 1029-UNK
                              1012-UNK 1021-UNK 1030-UNK
                               1013-UNK 1022-UNK 1031-UNK
                                1014-UNK 1023-UNK 1032-UNK
                                 1015-UNK 1024-UNK 1033-UNK

Chain X from PDB  Type:PROTEIN  Length:503
 aligned with PLXB1_HUMAN | O43157 from UniProtKB/Swiss-Prot  Length:2135

    Alignment length:567
                                  1572      1582      1592      1602      1612      1622      1632      1642      1652      1662      1672      1682      1692      1702      1712      1722      1732      1742      1752      1762      1772      1782      1792      1802      1812      1822      1832      1842      1852      1862      1872      1882      1892      1902      1912      1922      1932      1942      1952      1962      1972      1982      1992      2002      2012      2022      2032      2042      2052      2062      2072      2082      2092      2102      2112      2122       
         PLXB1_HUMAN   1563 IPFLDYKVYAERIFFPGHRESPLHRDLGVPESRRPTVEQGLGQLSNLLNSKLFLTKFIHTLESQRTFSARDRAYVASLLTVALHGKLEYFTDILRTLLSDLVAQYVAKNPKLMLRRTETVVEKLLTNWMSICLYTFVRDSVGEPLYMLFRGIKHQVDKGPVDSVTGKAKYTLNDNRLLREDVEYRPLTLNALLAVGPGAGEAQGVPVKVLDCDTISQAKEKMLDQLYKGVPLTQRPDPRTLDVEWRSGVAGHLILSDEDVTSEVQGLWRRLNTLQHYKVPDGATVALVPCLTKHVLRENQDYVPGERTPMLEDVDEGGIRPWHLVKPSDEPEPPRPRRGSLRGGERERAKAIPEIYLTRLLSMKGTLQKFVDDLFQVILSTSRPVPLAVKYFFDLLDEQAQQHGISDQDTIHIWKTNSLPLRFWINIIKNPQFVFDVQTSDNMDAVLLVIAQTFMDACTLADHKLGRDSPINKLLYARDIPRYKRMVERYYADIRQTVPASDQEMNSVLAELSWNYSGDLGARVALHELYKYINKYYDQIITALEEDGTAQKMQLGYRLQQIAAAVE 2129
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhh...--.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........................eeeeeee..-------...eeeeee...hhhhhhhhhhhhhh...hhhhh.hhh.eeeeee.....eeee........ee..eee.............eeeeee.--------------------------...eee......-----------------------.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...------.hhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.24a  PDB: X:1563-1618 (gaps) UniProt: 1546-1618  Exon 1.25  PDB: X:1619-1678 UniProt: 1619-1678              ----------------------Exon 1.26c  PDB: X:1701-1749 UniProt: 1701-1749  Exon 1.27b  PDB: X:1750-1806 (gaps) UniProt: 1750-1806   ----------------------------------Exon 1.28a  PDB: X:1841-1852 ---------------------------------------------------------Exon 1.30a  PDB: X:1927-1980 UniProt: 1927-1980       -------------------------------------------------Exon 1.31a            -------------------------Exon 1.33b               Exon 1.34c  PDB: X:2102-2129 Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------Exon 1.26a             ---------------------------------------------------------------------------------------------------------Exon 1.27d  PDB: X:1806-1840       ----------------------------Exon 1.29b  PDB: X:1879-1926 (gaps) UniProt: 1869-1926    -----------------------------------------------------Exon 1.30d  PDB: X:1980-2024 UniProt: 1980-2029   ---------------------Exon 1.32a                ----------------------------------------------------- Transcript 1 (2)
                3hm6 X 1563 IPFLDYKVYAERIFFPGH--SPLHRDLGVPESRRPTVEQGLGQLSNLLNSKLFLTKFIHTLETQRTFSARDRAYVASLLTVALHGKLEYFTDILRTLLSDLVAQYVAKNPKLMLRRTETVVEKLLTNWMSICLYTFVRDSVGEPLYMLFRGIKHQVDKGPVDSVTGKAKYTLNDNRLLREDVEYRPLTLNALLA-------AQGVPVKVLDCDTISQAKEKMLDQLYKGVPLTQRPDPRTLDVEWRSGVAGHLILSDEDVTSEVQGLWRRLNTLQHYKVPDGATVALVPC--------------------------GGIRPWHLVKPS-----------------------IPEIYLTRLLSMKGTLQKFVDDLFQVILSTSRPVPLAVKYFFDLLDEQAQQHGISDQDTIHIWKTNSLPLRFWINIIKNPQFVFDVQTSDNMDAVLLVIAQTFMDACTLAD------SPINKLLYARDIPRYKRMVERYYADIRQTVPASDQEMNSVLAELSWNYSGDLGARVALHELYKYINKYYDQIITALEEDGTAQKMQLGYRLQQIAAAVE 2129
                                  1572       | -|     1592      1602      1612      1622      1632      1642      1652      1662      1672      1682      1692      1702      1712      1722      1732      1742      1752   |     - |    1772      1782      1792      1802      1812      1822      1832      1842      1852         -         -      1882       | -         -         - |    1922      1932      1942      1952      1962      1972      1982      1992      2002      2012      2022 |    2032      2042      2052      2062      2072      2082      2092      2102      2112      2122       
                                          1580  |                                                                                                                                                                         1756    1764                                                                                    1852                       1879       1890                    1914                                                                                                          2024   2031                                                                                                  
                                             1583                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  

   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  (0, 0)

(no "SCOP Domain" information available for 3HM6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3HM6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HM6)

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X   (PLXB1_HUMAN | O43157)
molecular function
    GO:0032794    GTPase activating protein binding    Interacting selectively and non-covalently with a GTPase activating protein.
    GO:0005096    GTPase activator activity    Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
    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:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
    GO:0017154    semaphorin receptor activity    Combining with a semaphorin, and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
    GO:0030215    semaphorin receptor binding    Interacting selectively and non-covalently with semaphorin receptors.
    GO:0004888    transmembrane signaling receptor activity    Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction.
biological process
    GO:0048675    axon extension    Long distance growth of a single axon process involved in cellular development.
    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: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:0007162    negative regulation of cell adhesion    Any process that stops, prevents, or reduces the frequency, rate or extent of cell adhesion.
    GO:0033689    negative regulation of osteoblast proliferation    Any process that stops, prevents or reduces the rate or extent of osteoblast proliferation.
    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:0043931    ossification involved in bone maturation    The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone, involved in the progression of the skeleton from its formation to its mature state.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0050772    positive regulation of axonogenesis    Any process that activates or increases the frequency, rate or extent of axonogenesis.
    GO:0014068    positive regulation of phosphatidylinositol 3-kinase signaling    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
    GO:0043087    regulation of GTPase activity    Any process that modulates the rate of GTP hydrolysis by a GTPase.
    GO:0030334    regulation of cell migration    Any process that modulates the frequency, rate or extent of cell migration.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0051493    regulation of cytoskeleton organization    Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures.
    GO:0071526    semaphorin-plexin signaling pathway    A series of molecular signals generated as a consequence of a semaphorin receptor (composed of a plexin and a neurophilin) binding to a semaphorin ligand.
    GO:1902287    semaphorin-plexin signaling pathway involved in axon guidance    Any semaphorin-plexin signaling pathway that is involved in axon guidance.
    GO:1900220    semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis    Any semaphorin-plexin signaling pathway that contributes to bone trabecula morphogenesis.
    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.
cellular component
    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:0005887    integral component of plasma membrane    The component of the plasma 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.
    GO:0002116    semaphorin receptor complex    A stable binary complex of a neurophilin and a plexin, together forming a functional semaphorin receptor.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PLXB1_HUMAN | O431572jph 2os6 2r2o 2rex 3ol2 3su8 3sua 5b4w

(-) Related Entries Specified in the PDB File

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