Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF AN ALKA HOST/GUEST COMPLEX 2'-FLUORO-2'-DEOXY-1,N6-ETHENOADENINE:THYMINE BASE PAIR
 
Authors :  B. R. Bowman, S. Lee, S. Wang, G. L. Verdine
Date :  22 Apr 08  (Deposition) - 02 Sep 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Alka, 2'-Fluoro-2'-Deoxy-1, N6-Ethenoadenine, Dna Repair, Host/Guest Complex, Dna Structure, Dna Damage, Hydrolase, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. R. Bowman, S. Lee, S. Wang, G. L. Verdine
Structure Of The E. Coli Dna Glycosylase Alka Bound To The Ends Of Duplex Dna: A System For The Structure Determination Of Lesion-Containing Dna.
Structure V. 16 1166 2008
PubMed-ID: 18682218  |  Reference-DOI: 10.1016/J.STR.2008.04.012
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA-3-METHYLADENINE GLYCOSYLASE 2
    Chains: A, B, C, D
    EC Number: 3.2.2.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30
    Expression System Strain: BL21(DE3)
    Expression System Vector Type: PLASMID
    Gene: ALKA, AIDA
    Organism Scientific: ESCHERICHIA COLI
    Synonym: DNA-3-METHYLADENINE GLYCOSYLASE II, 3- METHYLADENINE-DNA GLYCOSYLASE II, INDUCIBLE, TAG II, DNA-3- METHYLADENINE GLYCOSIDASE II
 
Molecule 2 - DNA (5'-D(*DGP*DAP*DCP*DAP*DTP*DGP*DAP*(2FE) P*DTP*DGP*DCP*DC)-3')
    Chains: E, G
    Engineered: YES
    Other Details: 2'-FLUORO-2'-DEOXY-1,N6-ETHENOADENINE CONTAINING DNA
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(*DGP*DGP*DCP*DAP*DTP*DTP*DCP*DAP*DTP*DGP*DTP*DC)-3')
    Chains: F, H
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit : ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
12FE2Mod. Nucleotide2'-FLUORO-2'-DEOXY-1,N6-ETHENOADENINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR B:249 , DA E:7 , DT E:9 , DA F:17 , DT F:18 , DT F:19BINDING SITE FOR RESIDUE 2FE E 8
2AC2SOFTWARETHR C:249 , DA G:7 , DT G:9 , DA H:17 , DT H:18BINDING SITE FOR RESIDUE 2FE G 8

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Pro A:8 -Pro A:9
2Lys A:261 -Pro A:262
3Pro B:8 -Pro B:9
4Lys B:261 -Pro B:262
5Pro C:8 -Pro C:9
6Lys C:261 -Pro C:262
7Pro D:8 -Pro D:9
8Lys D:261 -Pro D:262

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALKYLBASE_DNA_GLYCOSPS00516 Alkylbase DNA glycosidases alkA family signature.3MG2_ECOLI214-238
 
 
 		  4A:214-238
B:214-238
C:214-238
D:214-238

(-) Exons   (0, 0)

(no "Exon" information available for 3CWU)

(-) 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:282
 aligned with 3MG2_ECOLI | P04395 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:282
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280  
           3MG2_ECOLI     1 MYTLNWQPPYDWSWMLGFLAARAVSSVETVADSYYARSLAVGEYRGVVTAIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGRLGAARPGLRLPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRFPGMTPAQIRRYAERWKPWRSYALLHIWYTEGWQPDEA 282
               SCOP domains d3cwua2 A:1-99 3-Methyladenine DNA glycosylase II (gene alkA or aidA)                              d3cwua1 A:100-282 3-Methyladenine DNA glycosylase II (gene alkA or aidA)                                                                                                                SCOP domains
               CATH domains 3cwuA01 A:1-112 DNA-3-methyladenine glycosylase ii                                                              3cwuA02 A:113-230 Hypothetical protein; domain 2                                                                      3cwuA03 A:231-282                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee.....hhhhhhhhhhh......eee....eeeeeee..eeeeeeeeee....eeeeee.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.............hhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhhhhhh....hhhhhhhhhhhhh.........hhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ALKYLBASE_DNA_GLYCOS     -------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cwu A   1 MYTLNWQPPYDWSWMLGFLAARAVSSVETVADSYYARSLAVGEYRGVVTAIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGRLGAARPGLRLPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRFPGMTPAQIRRYAERWKPWRSYALLHIWYTEGWQPDEA 282
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280  


Chain B from PDB  Type:PROTEIN  Length:282
 aligned with 3MG2_ECOLI | P04395 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:282
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280  
           3MG2_ECOLI     1 MYTLNWQPPYDWSWMLGFLAARAVSSVETVADSYYARSLAVGEYRGVVTAIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGRLGAARPGLRLPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRFPGMTPAQIRRYAERWKPWRSYALLHIWYTEGWQPDEA 282
               SCOP domains d3cwub2 B:1-99 3-Methyladenine DNA glycosylase II (gene alkA or aidA)                              d3cwub1 B:100-282 3-Methyladenine DNA glycosylase II (gene alkA or aidA)                                                                                                                SCOP domains
               CATH domains 3cwuB01 B:1-112 DNA-3-methyladenine glycosylase ii                                                              3cwuB02 B:113-230 Hypothetical protein; domain 2                                                                      3cwuB03 B:231-282                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee.....hhhhhhhhhhhh.....eeee..eeeeeeee..eeeeeeeeee....eeeeee.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhee.......ee..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhh.....hhhhhhhhhhhhh.........hhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ALKYLBASE_DNA_GLYCOS     -------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cwu B   1 MYTLNWQPPYDWSWMLGFLAARAVSSVETVADSYYARSLAVGEYRGVVTAIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGRLGAARPGLRLPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRFPGMTPAQIRRYAERWKPWRSYALLHIWYTEGWQPDEA 282
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280  


Chain C from PDB  Type:PROTEIN  Length:282
 aligned with 3MG2_ECOLI | P04395 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:282
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280  
           3MG2_ECOLI     1 MYTLNWQPPYDWSWMLGFLAARAVSSVETVADSYYARSLAVGEYRGVVTAIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGRLGAARPGLRLPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRFPGMTPAQIRRYAERWKPWRSYALLHIWYTEGWQPDEA 282
               SCOP domains d3cwuc2 C:1-99 3-Methyladenine DNA glycosylase II (gene alkA or aidA)                              d3cwuc1 C:100-282 3-Methyladenine DNA glycosylase II (gene alkA or aidA)                                                                                                                SCOP domains
               CATH domains 3cwuC01 C:1-112 DNA-3-methyladenine glycosylase ii                                                              3cwuC02 C:113-230 Hypothetical protein; domain 2                                                                      3cwuC03 C:231-282                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee.....hhhhhhhhhhhh.....eee....eeeeeee..eeeeeeeeeehhh.eeeeee.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.............hhhhhh..hhhhhhh...hhhhhhhhhhhhhhhhhh........hhhhhhhhhh.....hhhhhhhhhhhhh.........hhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ALKYLBASE_DNA_GLYCOS     -------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cwu C   1 MYTLNWQPPYDWSWMLGFLAARAVSSVETVADSYYARSLAVGEYRGVVTAIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGRLGAARPGLRLPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRFPGMTPAQIRRYAERWKPWRSYALLHIWYTEGWQPDEA 282
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280  


Chain D from PDB  Type:PROTEIN  Length:282
 aligned with 3MG2_ECOLI | P04395 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:282
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280  
           3MG2_ECOLI     1 MYTLNWQPPYDWSWMLGFLAARAVSSVETVADSYYARSLAVGEYRGVVTAIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGRLGAARPGLRLPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRFPGMTPAQIRRYAERWKPWRSYALLHIWYTEGWQPDEA 282
               SCOP domains d3cwud2 D:1-99 3-Methyladenine DNA glycosylase II (gene alkA or aidA)                              d3cwud1 D:100-282 3-Methyladenine DNA glycosylase II (gene alkA or aidA)                                                                                                                SCOP domains
               CATH domains 3cwuD01 D:1-112 DNA-3-methyladenine glycosylase ii                                                              3cwuD02 D:113-230 Hypothetical protein; domain 2                                                                      3cwuD03 D:231-282                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee.....hhhhhhhhhhhh.....eeee..eeeeeeee..eeeeeeeeee....eeeeee.hhhh.hhhhhhhhhhhhhh...hhhhhhhhhh...............hhhhhhhhhhh....hhhhhhhhhhhhhhhhhee.......ee..hhhhhhh.hhhhhhh...hhhhhhhhhhhhhhh...........hhhhhhhhhhh....hhhhhhhhhhhh..........hhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ALKYLBASE_DNA_GLYCOS     -------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cwu D   1 MYTLNWQPPYDWSWMLGFLAARAVSSVETVADSYYARSLAVGEYRGVVTAIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGRLGAARPGLRLPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRFPGMTPAQIRRYAERWKPWRSYALLHIWYTEGWQPDEA 282
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280  


Chain E from PDB  Type:DNA  Length:12
                                            
                 3cwu E   1 GACATGAxTGCC  12
                                   |10  
                                   8-2FE


Chain F from PDB  Type:DNA  Length:12
                                            
                 3cwu F  14 GGCATTCATGTC  25
                                    23  


Chain G from PDB  Type:DNA  Length:12
                                            
                 3cwu G   1 GACATGAxTGCC  12
                                   |10  
                                   8-2FE


Chain H from PDB  Type:DNA  Length:12
                                            
                 3cwu H  14 GGCATTCATGTC  25
                                    23
   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  (2, 8)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (3, 12)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (3MG2_ECOLI | P04395)
molecular function
    GO:0008725    DNA-3-methyladenine glycosylase activity    Catalysis of the reaction: DNA containing 3-methyladenine + H2O = DNA with abasic site + 3-methyladenine. This reaction is the hydrolysis of DNA by cleavage of the N-C1' glycosidic bond between the damaged DNA 3-methyladenine and the deoxyribose sugar to remove the 3-methyladenine, leaving an abasic site.
    GO:0052822    DNA-3-methylguanine glycosylase activity    Catalysis of the reaction: DNA containing 3-methylguanine + H2O = DNA with abasic site + 3-methylguanine. This reaction is the hydrolysis of DNA by cleavage of the N-C1' glycosidic bond between the damaged DNA 3-methylguanine and the deoxyribose sugar to remove the 3-methylguanine, leaving an abasic site.
    GO:0052821    DNA-7-methyladenine glycosylase activity    Catalysis of the reaction: DNA containing 7-methyladenine + H2O = DNA with abasic site + 7-methyladenine. This reaction is the hydrolysis of DNA by cleavage of the N-C1' glycosidic bond between the damaged DNA 7-methyladenine and the deoxyribose sugar to remove the 7-methyladenine, leaving an abasic site.
    GO:0043916    DNA-7-methylguanine glycosylase activity    Catalysis of the reaction: DNA containing 7-methylguanine + H2O = DNA with abasic site + 7-methylguanine. This reaction is the hydrolysis of DNA by cleavage of the N-C1' glycosidic bond between the damaged DNA 7-methylguanine and the deoxyribose sugar to remove the 7-methylguanine, leaving an abasic site.
    GO:0003905    alkylbase DNA N-glycosylase activity    Catalysis of the reaction: DNA with alkylated base + H2O = DNA with abasic site + alkylated base. This reaction is the hydrolysis of DNA by cleavage of the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar to remove an alkylated base, leaving an apyrimidinic or apurinic site.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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.
biological process
    GO:0006307    DNA dealkylation involved in DNA repair    The repair of alkylation damage, e.g. the removal of the alkyl group at the O6-position of guanine by O6-alkylguanine-DNA alkyltransferase (AGT).
    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: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: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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    2FE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Lys A:261 - Pro A:262   [ RasMol ]  
    Lys B:261 - Pro B:262   [ RasMol ]  
    Lys C:261 - Pro C:262   [ RasMol ]  
    Lys D:261 - Pro D:262   [ RasMol ]  
    Pro A:8 - Pro A:9   [ RasMol ]  
    Pro B:8 - Pro B:9   [ RasMol ]  
    Pro C:8 - Pro C:9   [ RasMol ]  
    Pro D:8 - Pro D:9   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3cwu
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  3MG2_ECOLI | P04395
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.2.2.21
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  3MG2_ECOLI | P04395
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        3MG2_ECOLI | P04395: 1diz 1mpg 1pvs 3cvs 3cvt 3cw7 3cwa 3cws 3cwt 3d4v 3ogd 3oh6 3oh9

(-) Related Entries Specified in the PDB File

3cvs 3cvt 3cw7 3cwa 3cws 3cwt