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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BARD1 BRCT DOMAINS
 
Authors :  G. Birrane, A. K. Varma, A. Soni, J. A. A. Ladias
Date :  07 Nov 06  (Deposition) - 12 Jun 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Brct, Ring Finger, Brca1, Zinc-Binding Protein, Ubiquitin Ligase, Antitumor Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Birrane, A. K. Varma, A. Soni, J. A. Ladias
Crystal Structure Of The Bard1 Brct Domains.
Biochemistry V. 46 7706 2007
PubMed-ID: 17550235  |  Reference-DOI: 10.1021/BI700323T

(-) Compounds

Molecule 1 - BRCA1-ASSOCIATED RING DOMAIN PROTEIN 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET-6H
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentBRCT DOMAIN
    GeneBARD1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBARD-1

 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  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2EDO5Ligand/Ion1,2-ETHANEDIOL
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO3Ligand/Ion1,2-ETHANEDIOL
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3SO41Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH B:63 , HOH B:277 , SER B:575 , GLY B:576 , THR B:617 , LYS B:619BINDING SITE FOR RESIDUE SO4 B 301
02AC2SOFTWAREHOH A:10 , SER A:575 , GLY A:576 , THR A:617 , LYS A:619BINDING SITE FOR RESIDUE SO4 A 302
03AC3SOFTWAREASN A:718BINDING SITE FOR RESIDUE CL A 304
04AC4SOFTWARELYS B:757BINDING SITE FOR RESIDUE CL B 306
05AC5SOFTWAREASP B:710 , SER B:711 , GLN B:715BINDING SITE FOR RESIDUE CL B 305
06AC6SOFTWAREHOH A:280 , PRO A:707 , SER A:711 , ASP A:712 , VAL A:713 , GLN A:735BINDING SITE FOR RESIDUE EDO A 307
07AC7SOFTWAREPHE B:672 , ASP B:673 , GLY B:674 , CYS B:675 , GLY B:699 , GLY B:700 , GLN B:701BINDING SITE FOR RESIDUE EDO B 308
08AC8SOFTWAREHOH A:280 , LEU A:703 , SER A:704 , ARG A:705BINDING SITE FOR RESIDUE EDO A 309
09AC9SOFTWARETHR A:617 , LEU A:618 , MET A:621 , HIS A:686 , ASN A:690BINDING SITE FOR RESIDUE EDO A 310
10BC1SOFTWAREARG A:658 , TYR B:678BINDING SITE FOR RESIDUE EDO B 311

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2NTE)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2NTE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 10)

Asymmetric Unit (5, 10)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_038372C645RBARD1_HUMANPolymorphism34744268A/BC645R
2UniProtVAR_010359R658CBARD1_HUMANPolymorphism3738888A/BR658C
3UniProtVAR_010360V695LBARD1_HUMANUnclassified111367604A/BV695L
4UniProtVAR_028309S728FBARD1_HUMANPolymorphism13389423A/BS728F
5UniProtVAR_010361S761NBARD1_HUMANUnclassified142155101A/BS761N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_038372C645RBARD1_HUMANPolymorphism34744268AC645R
2UniProtVAR_010359R658CBARD1_HUMANPolymorphism3738888AR658C
3UniProtVAR_010360V695LBARD1_HUMANUnclassified111367604AV695L
4UniProtVAR_028309S728FBARD1_HUMANPolymorphism13389423AS728F
5UniProtVAR_010361S761NBARD1_HUMANUnclassified142155101AS761N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_038372C645RBARD1_HUMANPolymorphism34744268BC645R
2UniProtVAR_010359R658CBARD1_HUMANPolymorphism3738888BR658C
3UniProtVAR_010360V695LBARD1_HUMANUnclassified111367604BV695L
4UniProtVAR_028309S728FBARD1_HUMANPolymorphism13389423BS728F
5UniProtVAR_010361S761NBARD1_HUMANUnclassified142155101BS761N

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

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BRCTPS50172 BRCT domain profile.BARD1_HUMAN570-653
 
667-777
 
  4A:570-653
B:570-653
A:667-777
B:667-777
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BRCTPS50172 BRCT domain profile.BARD1_HUMAN570-653
 
667-777
 
  2A:570-653
-
A:667-777
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BRCTPS50172 BRCT domain profile.BARD1_HUMAN570-653
 
667-777
 
  2-
B:570-653
-
B:667-777

(-) Exons   (4, 8)

Asymmetric Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002609471aENSE00002144066chr2:215674428-215674136293BARD1_HUMAN1-53530--
1.2aENST000002609472aENSE00001653146chr2:215661841-21566178557BARD1_HUMAN53-72200--
1.3ENST000002609473ENSE00001671724chr2:215657169-215657021149BARD1_HUMAN72-122510--
1.4bENST000002609474bENSE00001630355chr2:215646233-215645284950BARD1_HUMAN122-4383170--
1.5ENST000002609475ENSE00001596052chr2:215634036-21563395681BARD1_HUMAN439-465270--
1.6ENST000002609476ENSE00001792455chr2:215632378-215632206173BARD1_HUMAN466-523580--
1.7aENST000002609477aENSE00001641114chr2:215617279-215617171109BARD1_HUMAN523-559370--
1.8aENST000002609478aENSE00001634739chr2:215610578-215610446133BARD1_HUMAN560-604452A:568-604
B:569-604
37
36
1.9ENST000002609479ENSE00001780119chr2:215609883-21560979193BARD1_HUMAN604-635322A:604-635
B:604-635
32
32
1.11cENST0000026094711cENSE00002150576chr2:215595232-21559513598BARD1_HUMAN635-667332A:635-667
B:635-667
33
33
1.13eENST0000026094713eENSE00001814041chr2:215593732-2155903703363BARD1_HUMAN668-7771102A:668-777
B:668-777
110
110

(-) 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:210
 aligned with BARD1_HUMAN | Q99728 from UniProtKB/Swiss-Prot  Length:777

    Alignment length:210
                                   577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777
          BARD1_HUMAN   568 GPLVLIGSGLSSEQQKMLSELAVILKAKKYTEFDSTVTHVVVPGDAVQSTLKCMLGILNGCWILKFEWVKACLRRKVCEQEEKYEIPEGPRRSRLNREQLLPKLFDGCYFYLWGTFKHHPKDNLIKLVTAGGGQILSRKPKPDSDVTQTINTVAYHARPDSDQRFCTQYIIYEDLCNYHPERVRQGKVWKAPSSWFIDCVMSFELLPLDS 777
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2nteA01 A:568-667  [code=3.40.50.10190, no name defined]                                            2nteA02 A:668-771  [code=3.40.50.10190, no name defined]                                                ------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee...hhhhhhhhhhhhhhh..eee........eeee.......hhhhhhhhhh..eeeehhhhhhhhhhh...hhhhh...hhhhhhhhhhhh.........eeee.......hhhhhhhhhhhh..eee....hhhhhhhhh...........hhhhh..eeeee...........ee..eeeeehhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------R------------C------------------------------------L--------------------------------F--------------------------------N---------------- SAPs(SNPs)
                    PROSITE --BRCT  PDB: A:570-653 UniProt: 570-653                                               -------------BRCT  PDB: A:667-777 UniProt: 667-777                                                                           PROSITE
           Transcript 1 (1) Exon 1.8a  PDB: A:568-604            ------------------------------Exon 1.11c  PDB: A:635-667       Exon 1.13e  PDB: A:668-777 UniProt: 668-777                                                                    Transcript 1 (1)
           Transcript 1 (2) ------------------------------------Exon 1.9  PDB: A:604-635        ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2nte A 568 GPLVLIGSGLSSEQQKMLSELAVILKAKKYTEFDSTVTHVVVPGDAVQSTLKCMLGILNGCWILKFEWVKACLRRKVCEQEEKYEIPEGPRRSRLNREQLLPKLFDGCYFYLWGTFKHHPKDNLIKLVTAGGGQILSRKPKPDSDVTQTINTVAYHARPDSDQRFCTQYIIYEDLCNYHPERVRQGKVWKAPSSWFIDCVMSFELLPLDS 777
                                   577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777

Chain B from PDB  Type:PROTEIN  Length:209
 aligned with BARD1_HUMAN | Q99728 from UniProtKB/Swiss-Prot  Length:777

    Alignment length:209
                                   578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768         
          BARD1_HUMAN   569 PLVLIGSGLSSEQQKMLSELAVILKAKKYTEFDSTVTHVVVPGDAVQSTLKCMLGILNGCWILKFEWVKACLRRKVCEQEEKYEIPEGPRRSRLNREQLLPKLFDGCYFYLWGTFKHHPKDNLIKLVTAGGGQILSRKPKPDSDVTQTINTVAYHARPDSDQRFCTQYIIYEDLCNYHPERVRQGKVWKAPSSWFIDCVMSFELLPLDS 777
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2nteB01 B:569-667  [code=3.40.50.10190, no name defined]                                           2nteB02 B:668-771  [code=3.40.50.10190, no name defined]                                                ------ CATH domains
           Pfam domains (1) BRCT-2nteB01 B:569-640                                                  ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) BRCT-2nteB02 B:569-640                                                  ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..eeee...hhhhhhhhhhhhhhh..ee.........eeee.......hhhhhhhhhhh.eeeehhhhhhhhhhh...hhhhhh..hhhhhhhhhhhh.........eeee.......hhhhhhhhhhhh..ee........hhhhhhh..........hhhhh..eeeee...........ee..eeeeehhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------R------------C------------------------------------L--------------------------------F--------------------------------N---------------- SAPs(SNPs)
                    PROSITE -BRCT  PDB: B:570-653 UniProt: 570-653                                               -------------BRCT  PDB: B:667-777 UniProt: 667-777                                                                           PROSITE
           Transcript 1 (1) Exon 1.8a  PDB: B:569-604           ------------------------------Exon 1.11c  PDB: B:635-667       Exon 1.13e  PDB: B:668-777 UniProt: 668-777                                                                    Transcript 1 (1)
           Transcript 1 (2) -----------------------------------Exon 1.9  PDB: B:604-635        ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2nte B 569 PLVLIGSGLSSEQQKMLSELAVILKAKKYTEFDSTVTHVVVPGDAVQSTLKCMLGILNGCWILKFEWVKACLRRKVCEQEEKYEIPEGPRRSRLNREQLLPKLFDGCYFYLWGTFKHHPKDNLIKLVTAGGGQILSRKPKPDSDVTQTINTVAYHARPDSDQRFCTQYIIYEDLCNYHPERVRQGKVWKAPSSWFIDCVMSFELLPLDS 777
                                   578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768         

   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 2NTE)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Family: BRCT (35)
1aBRCT-2nteB01B:569-640
1bBRCT-2nteB02B:569-640

(-) Gene Ontology  (34, 34)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (BARD1_HUMAN | Q99728)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0019900    kinase binding    Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0004842    ubiquitin-protein transferase activity    Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0000729    DNA double-strand break processing    The 5' to 3' exonucleolytic resection of the DNA at the site of the break to form a 3' single-strand DNA overhang.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0000731    DNA synthesis involved in DNA repair    Synthesis of DNA that proceeds from the broken 3' single-strand DNA end and uses the homologous intact duplex as the template.
    GO:0007050    cell cycle arrest    A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
    GO:0006974    cellular response to DNA damage 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 stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0006303    double-strand break repair via nonhomologous end joining    The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0031441    negative regulation of mRNA 3'-end processing    Any process that stops, prevents, or reduces the frequency, rate or extent of mRNA 3'-end processing.
    GO:0046826    negative regulation of protein export from nucleus    Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of proteins from the nucleus into the cytoplasm.
    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:0045732    positive regulation of protein catabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0085020    protein K6-linked ubiquitination    A protein ubiquitination process in which a polymer of ubiquitin, formed by linkages between lysine residues at position 6 of the ubiquitin monomers, is added to a protein. K6-linked ubiquitination is involved in DNA repair.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0042325    regulation of phosphorylation    Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule.
    GO:1901796    regulation of signal transduction by p53 class mediator    Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
    GO:0000732    strand displacement    The rejection of the broken 3' single-strand DNA molecule that formed heteroduplex DNA with its complement in an intact duplex DNA. The Watson-Crick base pairing in the original duplex is restored. The rejected 3' single-strand DNA molecule reanneals with its original complement to reform two intact duplex molecules.
    GO:0001894    tissue homeostasis    A homeostatic process involved in the maintenance of an internal steady state within a defined tissue of an organism, including control of cellular proliferation and death and control of metabolic function.
cellular component
    GO:0070531    BRCA1-A complex    A protein complex that contains the BRCA1-BARD1 heterodimer, RAP80/UIMC1, BRCC3/BRCC36, BRE/BRCC45, FAM175A/CCDC98/Abraxas and MERIT40/NBA1, and specifically recognizes and binds K63-linked polyubiquitin chains present on histone H2A and H2AX at DNA damage sites.
    GO:0031436    BRCA1-BARD1 complex    A heterodimeric complex comprising BRCA1 and BARD1, which possesses ubiquitin ligase activity and is involved in genome maintenance, possibly by functioning in surveillance for DNA damage.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    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:0000151    ubiquitin ligase complex    A protein complex that includes a ubiquitin-protein ligase and enables ubiquitin protein ligase activity. The complex also contains other proteins that may confer substrate specificity on the complex.

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  BARD1_HUMAN | Q99728
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 Related Entries

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

UniProtKB/Swiss-Prot
        BARD1_HUMAN | Q997281jm7 2r1z 3c5r 3fa2

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2NTE)