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(-) Description

Title :  STRUCTURES OF TERNARY COMPLEXES OF RAT DNA POLYMERASE BETA, A DNA TEMPLATE-PRIMER, AND DDCTP
 
Authors :  H. Pelletier, M. R. Sawaya, A. Kumar, S. H. Wilson, J. Kraut
Date :  19 May 94  (Deposition) - 14 Dec 94  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,P,T
Keywords :  Protein-Dna Complex, Transferase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Pelletier, M. R. Sawaya, A. Kumar, S. H. Wilson, J. Kraut
Structures Of Ternary Complexes Of Rat Dna Polymerase Beta, A Dna Template-Primer, And Ddctp.
Science V. 264 1891 1994
PubMed-ID: 7516580
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(*GP*GP*GP*CP*GP*CP*CP*G)-3')
    ChainsT
    EngineeredYES
    SyntheticYES
 
Molecule 2 - DNA (5'-D(*CP*GP*GP*CP*GP*CP*C)-3')
    ChainsP
    EngineeredYES
    SyntheticYES
 
Molecule 3 - PROTEIN (DNA POLYMERASE BETA (E.C.2.7.7.7))
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit APT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1DCT1Ligand/Ion2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:180 , SER A:188 , ASP A:190 , ASP A:192 , DCT A:338 , HOH A:419BINDING SITE FOR RESIDUE MG A 339
2AC2SOFTWAREASP A:190 , ASP A:192 , ASP A:256 , DCT A:338BINDING SITE FOR RESIDUE MG A 340
3AC3SOFTWAREARG A:149 , GLY A:179 , SER A:180 , ARG A:183 , GLY A:189 , ASP A:190 , ASP A:192 , TYR A:271 , PHE A:272 , GLY A:274 , ASP A:276 , ASN A:279 , MG A:339 , MG A:340 , HOH A:408 , DC P:7 , DG T:4BINDING SITE FOR RESIDUE DCT A 338

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:274 -Ser A:275

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BPF)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DNA_POLYMERASE_XPS00522 DNA polymerase family X signature.DPOLB_RAT179-198  1A:179-198

(-) Exons   (14, 14)

Asymmetric/Biological Unit (14, 14)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000260391ENSRNOE00000186777chr16:73864707-7386477468DPOLB_RAT1-21211A:9-2113
1.2ENSRNOT000000260392ENSRNOE00000185461chr16:73864965-7386502258DPOLB_RAT21-40201A:21-4020
1.3ENSRNOT000000260393ENSRNOE00000185504chr16:73867557-7386762367DPOLB_RAT40-62231A:40-6223
1.4ENSRNOT000000260394ENSRNOE00000185543chr16:73869319-7386939375DPOLB_RAT63-87251A:63-8725
1.5ENSRNOT000000260395ENSRNOE00000186057chr16:73870085-7387014359DPOLB_RAT88-107201A:88-10720
1.6ENSRNOT000000260396ENSRNOE00000185607chr16:73871161-7387121050DPOLB_RAT107-124181A:107-12418
1.7ENSRNOT000000260397ENSRNOE00000185647chr16:73873715-7387376652DPOLB_RAT124-141181A:124-14118
1.8ENSRNOT000000260398ENSRNOE00000186149chr16:73875864-7387591855DPOLB_RAT141-159191A:141-15919
1.9ENSRNOT000000260399ENSRNOE00000186214chr16:73876001-7387607373DPOLB_RAT160-184251A:160-18425
1.10ENSRNOT0000002603910ENSRNOE00000185711chr16:73876683-7387675371DPOLB_RAT184-207241A:184-20724
1.11ENSRNOT0000002603911ENSRNOE00000185748chr16:73878874-7387896087DPOLB_RAT208-236291A:208-23629
1.12ENSRNOT0000002603912ENSRNOE00000185778chr16:73884550-7388461465DPOLB_RAT237-258221A:237-258 (gaps)22
1.13ENSRNOT0000002603913ENSRNOE00000186274chr16:73885616-73885755140DPOLB_RAT258-305481A:258-30548
1.14ENSRNOT0000002603914ENSRNOE00000235677chr16:73887775-738901132339DPOLB_RAT305-335311A:305-33531

(-) 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:324
 aligned with DPOLB_RAT | P06766 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:327
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       
            DPOLB_RAT     9 ETLNGGITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVTGIGPSAARKLVDEGIKTLEDLRKNEDKLNHHQRIGLKYFEDFEKRIPREEMLQMQDIVLNEVKKLDPEYIATVCGSFRRGAESSGDMDVLLTHPNFTSESSKQPKLLHRVVEQLQKVRFITDTLSKGETKFMGVCQLPSENDENEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEQDIFDYIQWRYREPKDRSE 335
               SCOP domains d2bpfa1 A:9-91 DNA polymerase beta, N-terminal (8 kD)-domain                       d2bpfa3 A:92-148 DNA polymerase beta                     d2bpfa4 A:149-335 DNA polymerase beta, catalytic (31 kD) fragment                                                                                                                           SCOP domains
               CATH domains 2bpfA01 A:9-91  [code=1.10.150.110, no name defined]                               2bpfA02 A:92-148                                         2bpfA03 A:149-271 Beta Polymerase, domain 2                                                                                2bpfA04 A:272-335 Beta Polymerase, domain 3                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.....hhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhh...eeeehhhhhh...ee..eeeeee...........hhhhhhhhhhhhh...eeeeeee...eeeeee......---....eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee....eee..............hhhhhhhhh.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYMERASE_X    ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1     ------------------Exon 1.3  PDB: A:40-62 Exon 1.4  PDB: A:63-87   Exon 1.5            ----------------Exon 1.7          ------------------------------------------Exon 1.10  PDB: A:184-20Exon 1.11  PDB: A:208-236    Exon 1.12             ----------------------------------------------Exon 1.14  PDB: A:305-335       Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.2            ------------------------------------------------------------------Exon 1.6          ----------------Exon 1.8           Exon 1.9  PDB: A:160-184 -------------------------------------------------------------------------Exon 1.13  PDB: A:258-305 UniProt: 258-305      ------------------------------ Transcript 1 (2)
                 2bpf A   9 ETLNGGITDMLVELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVTGIGPSAARKLVDEGIKTLEDLRKNEDKLNHHQRIGLKYFEDFEKRIPREEMLQMQDIVLNEVKKLDPEYIATVCGSFRRGAESSGDMDVLLTHPNFTSESSKQPKLLHRVVEQLQKVRFITDTLSKGETKFMGVCQLPSEN---EYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEQDIFDYIQWRYREPKDRSE 335
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238      |  -|      258       268       278       288       298       308       318       328       
                                                                                                                                                                                                                                                                      245 249                                                                                      

Chain P from PDB  Type:DNA  Length:7
                                       
                 2bpf P   1 CGGCGCC   7

Chain T from PDB  Type:DNA  Length:8
                                        
                 2bpf T   4 GGGCGCCG  11

   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  (3, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (4, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BPF)

(-) Gene Ontology  (37, 37)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DPOLB_RAT | P06766)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0034061    DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and a 3'hydroxyl group.
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
    GO:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008017    microtubule binding    Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    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:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0071897    DNA biosynthetic process    The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    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:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0006284    base-excision repair    In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
    GO:0006287    base-excision repair, gap-filling    Repair of the damaged strand by the combined action of an apurinic endouclease that degrades a few bases on the damaged strand and a polymerase that synthesizes a 'patch' in the 5' to 3' direction, using the undamaged strand as a template.
    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:0048872    homeostasis of number of cells    Any biological process involved in the maintenance of the steady-state number of cells within a population of cells.
    GO:0071707    immunoglobulin heavy chain V-D-J recombination    The process in which immunoglobulin heavy chain V, D, and J gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS).
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0008630    intrinsic apoptotic signaling pathway in response to DNA damage    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the detection of DNA damage, and ends when the execution phase of apoptosis is triggered.
    GO:0048535    lymph node development    The process whose specific outcome is the progression of lymph nodes over time, from their formation to the mature structure. A lymph node is a round, oval, or bean shaped structure localized in clusters along the lymphatic vessels, with a distinct internal structure including specialized vasculature and B- and T-zones for the activation of lymphocytes.
    GO:0051402    neuron apoptotic process    Any apoptotic process in a neuron, the basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
    GO:0006290    pyrimidine dimer repair    The repair of UV-induced T-T, C-T and C-C dimers.
    GO:0045471    response to ethanol    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ethanol stimulus.
    GO:0010332    response to gamma radiation    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a gamma radiation stimulus. Gamma radiation is a form of electromagnetic radiation (EMR) or light emission of a specific frequency produced from sub-atomic particle interaction, such as electron-positron annihilation and radioactive decay. Gamma rays are generally characterized as EMR having the highest frequency and energy, and also the shortest wavelength, within the electromagnetic radiation spectrum.
    GO:0055093    response to hyperoxia    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating increased oxygen tension.
    GO:0007435    salivary gland morphogenesis    The process in which the anatomical structures of the salivary gland are generated and organized.
    GO:0016445    somatic diversification of immunoglobulins    The somatic process that results in the generation of sequence diversity of immunoglobulins.
    GO:0016446    somatic hypermutation of immunoglobulin genes    Mutations occurring somatically that result in amino acid changes in the rearranged V regions of immunoglobulins.
    GO:0048536    spleen development    The process whose specific outcome is the progression of the spleen over time, from its formation to the mature structure. The spleen is a large vascular lymphatic organ composed of white and red pulp, involved both in hemopoietic and immune system functions.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005874    microtubule    Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
    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:0005876    spindle microtubule    Any microtubule that is part of a mitotic or meiotic spindle; anchored at one spindle pole.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DPOLB_RAT | P067661bno 1bnp 1bpb 1bpd 1bpe 1dk2 1dk3 1huo 1huz 1jn3 1nom 1rpl 1zqu 1zqv 1zqw 1zqx 1zqy 1zqz 2bpc 2bpg 2van 3k75 3lqc 3uxn 3uxo 3uxp 3v72 3v7j 3v7k 3v7l

(-) Related Entries Specified in the PDB File

2bpg 2BPF STRUCTURE IS VERY SIMILAR TO THE STRUCTURE IN PDB ENTRY 2BPG WITH THE FOLLOWING DIFFERENCES: (1) THE STRUCTURE IN THIS ENTRY CRYSTALLIZED IN SPACE GROUP P 61, WHEREAS THE STRUCTURE IN ENTRY 2BPG CRYSTALLIZED IN SPACE GROUP P 21. (2) THE STRUCTURE IN THIS ENTRY WAS DETERMINED AT 2.9 ANGSTROMS RESOLUTION, WHEREAS THE STRUCTURE IN ENTRY 2BPG WAS DETERMINED AT 3.6 ANGSTROMS RESOLUTION. (3) THE STRUCTURE IN THIS ENTRY HAS ONE MOLECULE IN THE ASYMMETRIC UNIT, WHEREAS THE STRUCTURE IN ENTRY 2BPG HAS TWO MOLECULES IN THE ASYMMETRIC UNIT. (4) THE POSITION OF THE 8 KD DOMAIN DIFFERS IN THE TWO ENTRIES. (5) THE STRUCTURE IN THIS ENTRY INCLUDES TWO CATALYTICALLY IMPORTANT MG++ IONS, WHEREAS THE STRUCTURE IN ENTRY 2BPG WAS NOT DETERMINED AT A HIGH ENOUGH RESOLUTION TO SEE EVIDENCE OF THE MG++ IONS IN THE ELECTRON DENSITY MAPS OF THE ACTIVE SITE, SO THEY ARE NOT INCLUDED IN THAT ENTRY.