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(-) Description

Title :  CRYSTAL FORM BH1
 
Authors :  S. Bailey, W. K. Eliason, T. A. Steitz
Date :  05 Sep 07  (Deposition) - 06 Nov 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (3x)
Keywords :  Helicase, Primase, Replication, Dnab, Dnag (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Bailey, W. K. Eliason, T. A. Steitz
Structure Of Hexameric Dnab Helicase And Its Complex With A Domain Of Dnag Primase
Science V. 318 459 2007
PubMed-ID: 17947583  |  Reference-DOI: 10.1126/SCIENCE.1147353

(-) Compounds

Molecule 1 - REPLICATIVE HELICASE
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneDNAB
    Organism ScientificGEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid1422
    SynonymDNAB HELICASE
 
Molecule 2 - DNAG PRIMASE, HELICASE BINDING DOMAIN
    ChainsC
    EC Number2.7.7.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentHELICASE BINDING DOMAIN
    GeneDNAG
    Organism ScientificGEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid1422

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (3x)ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 30)
No.NameCountTypeFull Name
1MSE18Mod. Amino AcidSELENOMETHIONINE
2SO412Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:211 , SER A:213 , GLY A:215 , LYS A:216 , THR A:217 , HOH A:1011BINDING SITE FOR RESIDUE SO4 A 500
2AC2SOFTWAREARG A:45 , ALA A:46 , ALA A:47BINDING SITE FOR RESIDUE SO4 A 1001
3AC3SOFTWAREARG A:370 , SER B:213 , GLY B:215 , LYS B:216 , THR B:217 , HOH B:1008BINDING SITE FOR RESIDUE SO4 B 500
4AC4SOFTWAREARG B:45 , ALA B:46 , ALA B:47BINDING SITE FOR RESIDUE SO4 B 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R6A)

(-) Cis Peptide Bonds  (17, 17)

Asymmetric Unit
No.Residues
1Arg A:8 -Ile A:9
2Glu A:133 -Asp A:134
3Gly A:157 -Ala A:158
4Asp A:180 -Gly A:181
5Ser A:198 -Gly A:199
6Gly A:384 -Ser A:385
7Arg B:61 -Gly B:62
8Glu B:133 -Asp B:134
9Gln B:152 -Arg B:153
10Arg B:153 -Lys B:154
11Ser B:198 -Gly B:199
12Val B:214 -Gly B:215
13Ala B:286 -Gly B:287
14Leu B:314 -Gly B:315
15Asp B:320 -Tyr B:321
16Gly C:486 -Gly C:487
17Gly C:487 -Arg C:488

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R6A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2R6A)

(-) Exons   (0, 0)

(no "Exon" information available for 2R6A)

(-) 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:420
 aligned with Q9X4C9_GEOSE | Q9X4C9 from UniProtKB/TrEMBL  Length:454

    Alignment length:434
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437    
         Q9X4C9_GEOSE     8 RIPPQSIEAEQAVLGAVFLDPAALVPASEILIPEDFYRAAHQKIFHAMLRVADRGEPVDLVTVTAELAASEQLEEIGGVSYLSELADAVPTAANVEYYARIVEEKSVLRRLIRTATSIAQDGYTREDEIDVLLDEADRKIMEVSQRKHSGAFKNIKDILVQTYDNIEMLHNRDGEITGIPTGFTELDRMTSGFQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSLEMSAQQLVMRMLCAEGNINAQNLRTGKLTPEDWGKLTMAMGSLSNAGIYIDDTPSIRVSDIRAKCRRLKQESGLGMIVIDYLQLIQGSGRSKENRQQEVSEISRSLKALARELEVPVIALSQLSRSVEQRQDKRPMMSDIRESGSIEQDADIVAFLYRDDYYNKDSENKNIIEIIIAKQRNGPVGTVQLAFIKEYNKFVNL 441
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhh......hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh...........hhhhhhhhh......eeeee.....hhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhh.....eeeeehhhhh.....----hhhhhhhhhhhhhhhhhhhh..eeeee.........---...hhhhhh..hhhhhh.eeeeeee...-------..eeeeeeeee.....eeeeeeee....eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r6a A   8 RIPPQSIEAEQAVLGAVFLDPAALVPASEILIPEDFYRAAHQKIFHAMLRVADRGEPVDLVTVTAELAASEQLEEIGGVSYLSELADAVPTAANVEYYARIVEEKSVLRRLIRTATSIAQDGYTREDEIDVLLDEADRKIMEVSQRKHSGAFKNIKDILVQTYDNIEMLHNRDGEITGIPTGFTELDRMTSGFQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSLEMSAQQLVMRMLCAEGNINAQNLRTGKLTPEDWGKLTMAMGSLSNAGIYIDDTPSIRVSDIRAKCRRLKQESGLGMIVIDYLQLIQGSGR----RQQEVSEISRSLKALARELEVPVIALSQLSRSVEQR---RPMMSDIRESGSIEQDADIVAFLYRDDY-------KNIIEIIIAKQRNGPVGTVQLAFIKEYNKFVNL 441
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327  |    337       347       357       367  |   |377       387       397   |     - |     417       427       437    
                                                                                                                                                                                                                                                                                                                                                            330  335                                370 374                        401     409                                

Chain B from PDB  Type:PROTEIN  Length:374
 aligned with Q9X4C9_GEOSE | Q9X4C9 from UniProtKB/TrEMBL  Length:454

    Alignment length:433
                                    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       338       348       358       368       378       388       398       408       418       428       438   
         Q9X4C9_GEOSE     9 IPPQSIEAEQAVLGAVFLDPAALVPASEILIPEDFYRAAHQKIFHAMLRVADRGEPVDLVTVTAELAASEQLEEIGGVSYLSELADAVPTAANVEYYARIVEEKSVLRRLIRTATSIAQDGYTREDEIDVLLDEADRKIMEVSQRKHSGAFKNIKDILVQTYDNIEMLHNRDGEITGIPTGFTELDRMTSGFQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSLEMSAQQLVMRMLCAEGNINAQNLRTGKLTPEDWGKLTMAMGSLSNAGIYIDDTPSIRVSDIRAKCRRLKQESGLGMIVIDYLQLIQGSGRSKENRQQEVSEISRSLKALARELEVPVIALSQLSRSVEQRQDKRPMMSDIRESGSIEQDADIVAFLYRDDYYNKDSENKNIIEIIIAKQRNGPVGTVQLAFIKEYNKFVNL 441
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) DnaB-2r6aB03 B:9-111                                                                                   ---------------------------------------------------------------        --DnaB_C-2r6aB01 B:185-441                                                                                                                                                                                                                                          Pfam domains (1)
           Pfam domains (2) DnaB-2r6aB04 B:9-111                                                                                   ---------------------------------------------------------------        --DnaB_C-2r6aB02 B:185-441                                                                                                                                                                                                                                          Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..........eehhhhhhhhhh...--------.......hhhhhhhhh......eeeeee....hhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhh..hhhhhhh...hhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhh...eeeeehhhhh------------hhhhhhhhhhhhhhhhh..eeeeee.-------------------------...eeee.--------------.eeeeeeee......eeeeeee....eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r6a B   9 IPPQSIEAEQAVLGAVFLDPAALVPASEILIPEDFYRAAHQKIFHAMLRVADRGEPVDLVTVTAELAASEQLEEIGGVSYLSELADAVPTAANVEYYARIVEEKSVLRRLIRTATSIAQDGYTREDEIDVLLDEADRKIMEVSQRKHSGAFKNIKDILVQTYDNIE--------ITGIPTGFTELDRMTSGFQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSLEMSAQQLVMRMLCAEGNINAQNLRTGKLTPEDWGKLTMAMGSLSNAGIYIDDTPSIRVSDIRAKCRRLKQESGLGMIVIDYLQLI------------EVSEISRSLKALARELEVPVIALSQL-------------------------DADIVAFL--------------IIEIIIAKQRNGPVGTVQLAFIKEYNKFVNL 441
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168     |   -    |  188       198       208       218       228       238       248       258       268       278       288       298       308       318      |  -       338       348       358    |    -         -         -|      | -         -  |    418       428       438   
                                                                                                                                                                                               174      183                                                                                                                                           325          338                      363                       389    396            411                              

Chain C from PDB  Type:PROTEIN  Length:141
 aligned with DNAG_GEOSE | Q9X4D0 from UniProtKB/Swiss-Prot  Length:597

    Alignment length:141
                                   464       474       484       494       504       514       524       534       544       554       564       574       584       594 
           DNAG_GEOSE   455 KLLPAFQNAERLLLAHMMRSRDVALVVQERIGGRFNIEEHRALAAYIYAFYEEGHEADPGALISRIPGELQPLASDVSLLLIADDVSEQELEDYIRHVLNRPKWLMLKVKEQEKTEAERRKDFLTAARIAKEMIEMKKMLS 595
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.....hhhhhh......hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r6a C 455 KLLPAFQNAERLLLAHmmRSRDVALVVQERIGGRFNIEEHRALAAYIYAFYEEGHEADPGALISRIPGELQPLASELSLLLIADDVSEQELEDYIRHVLNRPKWLmLKVKEQEKTEAERRKDFLTAARIAKEmIEmKKmLS 595
                                   464      |474       484       494       504       514       524       534       544       554     | 564       574       584  |  | 594 
                                          471-MSE                                                                                  560-MSE                    587-MSE |  
                                           472-MSE                                                                                                               590-MSE 
                                                                                                                                                                    593-MSE

   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 2R6A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2R6A)

(-) Pfam Domains  (2, 4)

Asymmetric Unit

(-) Gene Ontology  (19, 27)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9X4C9_GEOSE | Q9X4C9)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003678    DNA helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA helix.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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: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).
biological process
    GO:0032508    DNA duplex unwinding    The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands.
    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:0006269    DNA replication, synthesis of RNA primer    The synthesis of a short RNA polymer, usually 4-15 nucleotides long, using one strand of unwound DNA as a template; the RNA then serves as a primer from which DNA polymerases extend synthesis.
cellular component
    GO:1990077    primosome complex    Any of a family of protein complexes that form at the origin of replication or stalled replication forks and function in replication primer synthesis in all organisms. Early complexes initiate double-stranded DNA unwinding. The core unit consists of a replicative helicase and a primase. The helicase further unwinds the DNA and recruits the polymerase machinery. The primase synthesizes RNA primers that act as templates for complementary stand replication by the polymerase machinery. The primosome contains a number of associated proteins and protein complexes and contributes to the processes of replication initiation, lagging strand elongation, and replication restart.

Chain C   (DNAG_GEOSE | Q9X4D0)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003678    DNA helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA helix.
    GO:0003896    DNA primase activity    Catalysis of the synthesis of a short RNA primer on a DNA template, providing a free 3'-OH that can be extended by DNA-directed DNA polymerases.
    GO:0003899    DNA-directed 5'-3' RNA polymerase activity    Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0032508    DNA duplex unwinding    The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands.
    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:0006269    DNA replication, synthesis of RNA primer    The synthesis of a short RNA polymer, usually 4-15 nucleotides long, using one strand of unwound DNA as a template; the RNA then serves as a primer from which DNA polymerases extend synthesis.
cellular component
    GO:1990077    primosome complex    Any of a family of protein complexes that form at the origin of replication or stalled replication forks and function in replication primer synthesis in all organisms. Early complexes initiate double-stranded DNA unwinding. The core unit consists of a replicative helicase and a primase. The helicase further unwinds the DNA and recruits the polymerase machinery. The primase synthesizes RNA primers that act as templates for complementary stand replication by the polymerase machinery. The primosome contains a number of associated proteins and protein complexes and contributes to the processes of replication initiation, lagging strand elongation, and replication restart.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DNAG_GEOSE | Q9X4D01d0q 1z8s 2r6c 4m4w
UniProtKB/TrEMBL
        Q9X4C9_GEOSE | Q9X4C92r6c 2r6d 2r6e 4esv 4m4w

(-) Related Entries Specified in the PDB File

2r6c CRYSTAL FORM BH2
2r6d CRYSTAL FORM B1
2r6e CRYSTAL FORM B2