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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BROMODOMAIN OF HUMAN TRANSCRIPTION ACTIVATOR BRG1 (SMARCA4) IN COMPLEX WITH N-METHYL-2-PYRROLIDONE
 
Authors :  P. Filippakopoulos, I. Felletar, S. Picaud, T. Keates, J. Muniz, O. Gil F. Von Delft, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, C. Bountra, Structural Genomics Consortium (Sgc)
Date :  29 Nov 11  (Deposition) - 18 Jan 12  (Release) - 11 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Bromodomain, Atp-Dependent Helicase Smarca4, Brg1-Associated Factor 190A, Baf190A, Mitotic Growth And Transcription Activator, Protein Brg-1, Protein Brahma Homolog 1, Snf2-Beta, Swi/Snf-Related Matrix- Associated Actin-Dependent Regulator Of Chromatin Subfamily A Member 4, Structural Genomics Consortium, Sgc, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Filippakopoulos, S. Picaud, M. Mangos, T. Keates, J. P. Lambert, D. Barsyte-Lovejoy, I. Felletar, R. Volkmer, S. Muller, T. Pawson, A. C. Gingras, C. H. Arrowsmith, S. Knapp
Histone Recognition And Large-Scale Structural Analysis Of The Human Bromodomain Family.
Cell(Cambridge, Mass. ) V. 149 214 2012
PubMed-ID: 22464331  |  Reference-DOI: 10.1016/J.CELL.2012.02.013

(-) Compounds

Molecule 1 - TRANSCRIPTION ACTIVATOR BRG1
    ChainsA
    EC Number3.6.4.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)-R3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 1448-1569
    GeneBRG1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBRG1-ASSOCIATED FACTOR PROTEIN BRG-1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1MB31Ligand/Ion1-METHYLPYRROLIDIN-2-ONE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:58 , VAL A:1484 , PHE A:1485 , PHE A:1539 , ASN A:1540BINDING SITE FOR RESIDUE MB3 A 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BROMODOMAIN_2PS50014 Bromodomain profile.SMCA4_HUMAN1477-1547  1A:1477-1547
2BROMODOMAIN_1PS00633 Bromodomain signature.SMCA4_HUMAN1482-1539  1A:1482-1539

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003446261ENSE00001132251chr19:11071598-11071850253SMCA4_HUMAN-00--
1.3aENST000003446263aENSE00000874191chr19:11094797-11095049253SMCA4_HUMAN1-74740--
1.4ENST000003446264ENSE00000874194chr19:11095949-11096081133SMCA4_HUMAN75-119450--
1.5ENST000003446265ENSE00000874195chr19:11096865-11097269405SMCA4_HUMAN119-2541360--
1.6ENST000003446266ENSE00000874198chr19:11097581-1109767999SMCA4_HUMAN254-287340--
1.7ENST000003446267ENSE00000874199chr19:11098342-11098600259SMCA4_HUMAN287-373870--
1.8ENST000003446268ENSE00000874200chr19:11099993-11100119127SMCA4_HUMAN373-415430--
1.9ENST000003446269ENSE00001729313chr19:11101826-11101999174SMCA4_HUMAN416-473580--
1.10ENST0000034462610ENSE00000874205chr19:11105504-11105677174SMCA4_HUMAN474-531580--
1.11ENST0000034462611ENSE00001328899chr19:11106889-11107056168SMCA4_HUMAN532-587560--
1.12ENST0000034462612ENSE00000874208chr19:11107170-1110722051SMCA4_HUMAN588-604170--
1.13ENST0000034462613ENSE00000874209chr19:11113705-11113835131SMCA4_HUMAN605-648440--
1.14ENST0000034462614ENSE00000874210chr19:11114016-1111407358SMCA4_HUMAN648-667200--
1.15ENST0000034462615ENSE00000874211chr19:11118578-11118699122SMCA4_HUMAN668-708410--
1.16ENST0000034462616ENSE00000874212chr19:11121057-11121207151SMCA4_HUMAN708-758510--
1.17ENST0000034462617ENSE00000874213chr19:11123625-11123788164SMCA4_HUMAN759-813550--
1.18ENST0000034462618ENSE00000874214chr19:11129633-1112969967SMCA4_HUMAN813-835230--
1.19ENST0000034462619ENSE00001266976chr19:11130267-11130377111SMCA4_HUMAN836-872370--
1.20ENST0000034462620ENSE00001669212chr19:11132401-11132643243SMCA4_HUMAN873-953810--
1.21ENST0000034462621ENSE00000954162chr19:11134194-11134307114SMCA4_HUMAN954-991380--
1.22ENST0000034462622ENSE00000954163chr19:11135007-11135114108SMCA4_HUMAN992-1027360--
1.23ENST0000034462623ENSE00001621775chr19:11136098-1113618487SMCA4_HUMAN1028-1056290--
1.24ENST0000034462624ENSE00000954165chr19:11136976-1113702247SMCA4_HUMAN1057-1072160--
1.25ENST0000034462625ENSE00000954166chr19:11138460-11138626167SMCA4_HUMAN1072-1128570--
1.26ENST0000034462626ENSE00000954167chr19:11141406-11141569164SMCA4_HUMAN1128-1182550--
1.27ENST0000034462627ENSE00001671853chr19:11143966-11144193228SMCA4_HUMAN1183-1258760--
1.28ENST0000034462628ENSE00000954169chr19:11144443-1114454199SMCA4_HUMAN1259-1291330--
1.29ENST0000034462629ENSE00000954170chr19:11144799-1114487678SMCA4_HUMAN1292-1317260--
1.30ENST0000034462630ENSE00000954171chr19:11145590-11145808219SMCA4_HUMAN1318-1390730--
1.33bENST0000034462633bENSE00001413377chr19:11151983-11152236254SMCA4_HUMAN1391-1475851A:1447-147529
1.34aENST0000034462634aENSE00001360053chr19:11168931-11169039109SMCA4_HUMAN1475-1511371A:1475-151137
1.35ENST0000034462635ENSE00000954175chr19:11169464-11169565102SMCA4_HUMAN1512-1545341A:1512-154534
1.36ENST0000034462636ENSE00001360043chr19:11170429-11170561133SMCA4_HUMAN1546-1590451A:1546-156823
1.37ENST0000034462637ENSE00000954177chr19:11170721-11170863143SMCA4_HUMAN1590-1637480--
1.38ENST0000034462638ENSE00001360023chr19:11172460-11172958499SMCA4_HUMAN1638-1647100--

(-) 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 A from PDB  Type:PROTEIN  Length:122
 aligned with SMCA4_HUMAN | P51532 from UniProtKB/Swiss-Prot  Length:1647

    Alignment length:122
                                  1456      1466      1476      1486      1496      1506      1516      1526      1536      1546      1556      1566  
         SMCA4_HUMAN   1447 PAEKLSPNPPNLTKKMKKIVDAVIKYKDSSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLNDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFTSVRQKIEKED 1568
               SCOP domains d3uvda_ A: automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhh.......hhhhhhh.......hhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------BROMODOMAIN_2  PDB: A:1477-1547 UniProt: 1477-1547                     --------------------- PROSITE (1)
                PROSITE (2) -----------------------------------BROMODOMAIN_1  PDB: A:1482-1539 UniProt: 1482-1539        ----------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.33b  PDB: A:1447-1475 ------------------------------------Exon 1.35  PDB: A:1512-1545       Exon 1.36 [INCOMPLETE]  Transcript 1 (1)
           Transcript 1 (2) ----------------------------Exon 1.34a  PDB: A:1475-1511         --------------------------------------------------------- Transcript 1 (2)
                3uvd A 1447 MAEKLSPNPPNLTKKMKKIVDAVIKYKDSSSGRQLSEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLNDLEKDVMLLCQNAQTFNLEGSLIYEDSIVLQSVFTSVRQKIEKED 1568
                                  1456      1466      1476      1486      1496      1506      1516      1526      1536      1546      1556      1566  

   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/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (59, 59)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SMCA4_HUMAN | P51532)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0070182    DNA polymerase binding    Interacting selectively and non-covalently with a DNA polymerase.
    GO:0008094    DNA-dependent ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of single- or double-stranded DNA, and it drives another reaction.
    GO:0001164    RNA polymerase I CORE element sequence-specific DNA binding    Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase I transcription machinery. This site is often referred to as the CORE element. In mammalian cells, the CORE element functions in conjunction with the Upstream Control Element (UCE), while in fungi, protozoa, and plants, the CORE element functions without a UCE.
    GO:0000978    RNA polymerase II core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
    GO:0000980    RNA polymerase II distal enhancer sequence-specific DNA binding    Interacting selectively and non-covalently with a RNA polymerase II (Pol II) distal enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of some promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter.
    GO:0001105    RNA polymerase II transcription coactivator activity    Interacting selectively and non-covalently with an RNA polymerase II (RNAP II) regulatory transcription factor and also with the RNAP II basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between activating transcription factors and the basal RNAP II transcription machinery.
    GO:0030957    Tat protein binding    Interacting selectively and non-covalently with Tat, a viral transactivating regulatory protein from the human immunodeficiency virus, or the equivalent protein from another virus.
    GO:0050681    androgen receptor binding    Interacting selectively and non-covalently with an androgen receptor.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016817    hydrolase activity, acting on acid anhydrides    Catalysis of the hydrolysis of any acid anhydride.
    GO:0070577    lysine-acetylated histone binding    Interacting selectively and non-covalently with a histone in which a lysine residue has been modified by acetylation.
    GO:0031492    nucleosomal DNA binding    Interacting selectively and non-covalently with the DNA portion of a nucleosome.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0002039    p53 binding    Interacting selectively and non-covalently with one of the p53 family of proteins.
    GO:0047485    protein N-terminus binding    Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
    GO:0003714    transcription corepressor activity    Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
    GO:0043044    ATP-dependent chromatin remodeling    Dynamic structural changes to eukaryotic chromatin that require energy from the hydrolysis of ATP, ranging from local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation, mediated by ATP-dependent chromatin-remodelling factors.
    GO:1904837    beta-catenin-TCF complex assembly    The aggregation, arrangement and bonding together of a set of components to form a beta-catenin-TCF complex.
    GO:0006338    chromatin remodeling    Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
    GO:2000134    negative regulation of G1/S transition of mitotic cell cycle    Any cell cycle regulatory process that prevents the commitment of a cell from G1 to S phase of the mitotic cell cycle.
    GO:0060766    negative regulation of androgen receptor signaling pathway    Any process that decreases the rate, frequency, or extent of the androgen receptor signaling pathway.
    GO:0030308    negative regulation of cell growth    Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0007070    negative regulation of transcription from RNA polymerase II promoter during mitotic cell cycle    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter that occurs during the mitotic cell cycle.
    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:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0003407    neural retina development    The progression of the neural retina over time from its initial formation to the mature structure. The neural retina is the part of the retina that contains neurons and photoreceptor cells.
    GO:0006337    nucleosome disassembly    The controlled breakdown of nucleosomes, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
    GO:0043923    positive regulation by host of viral transcription    Any process in which a host organism activates or increases the frequency, rate or extent of viral transcription, the synthesis of either RNA on a template of DNA or DNA on a template of RNA.
    GO:0030177    positive regulation of Wnt signaling pathway    Any process that activates or increases the frequency, rate or extent of Wnt signal transduction.
    GO:1902661    positive regulation of glucose mediated signaling pathway    Any process that activates or increases the frequency, rate or extent of glucose mediated signaling pathway.
    GO:1902895    positive regulation of pri-miRNA transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of pri-miRNA transcription from RNA polymerase II promoter.
    GO:0051091    positive regulation of sequence-specific DNA binding transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    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:1901838    positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter    Any process that activates or increases the frequency, rate or extent of transcription of nuclear large rRNA transcript from RNA polymerase I 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:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007286    spermatid development    The process whose specific outcome is the progression of a spermatid over time, from its formation to the mature structure.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0016514    SWI/SNF complex    A SWI/SNF-type complex that contains nine or more proteins, including both conserved (core) and nonconserved components; the Swi2/Snf2 ATPase is one of the core components.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0071565    nBAF complex    A SWI/SNF-type complex that is found in post-mitotic neurons, and in human contains actin and proteins encoded by the ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, DPF1/BAF45B, DPF3/BAF45C, ACTL6B/BAF53B genes. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth.
    GO:0071564    npBAF complex    A SWI/SNF-type complex that is found in neural stem or progenitor cells, and in human contains actin and proteins encoded by the ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, PHF10/BAF45A, ACTL6A/BAF53A genes. The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells.
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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  SMCA4_HUMAN | P51532
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SMCA4_HUMAN | P515322grc 2h60 5dkd 5ea1

(-) Related Entries Specified in the PDB File

3uv2 3uv4 3uv5 3uvw 3uvx 3uvy 3uw9