Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
(-)Biological Unit 5
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)
Image Biological Unit 5
Biological Unit 5  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF UVRA2 FROM DEINOCOCCUS RADIODURANS
 
Authors :  J. Timmins, E. Gordon, S. Caria, G. Leonard, M. S. Kuo, V. Monchois, S. Mc
Date :  31 Oct 07  (Deposition) - 16 Dec 08  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (2x)
Biol. Unit 3:  A  (1x)
Biol. Unit 4:  B  (1x)
Biol. Unit 5:  C  (1x)
Keywords :  Dna-Binding Protein, Nucleotide-Binding, Zinc-Binding Domain, Sos Response, Metal-Binding, Excision Nuclease, Zinc-Finger, Atp- Binding, Dna-Binding, Dna Excision, Zinc, Cytoplasm, Dna Damage, Dna Repair, Abc Protein Dna-Binding Protein, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Timmins, E. Gordon, S. Caria, G. Leonard, S. Acajjaoui, M. S. Kuo, V. Monchois, S. Mcsweeney
Structural And Mutational Analyses Of Deinococcus Radiodurans Uvra2 Provide Insight Into Dna Binding And Damage Recognition By Uvras.
Structure V. 17 547 2009
PubMed-ID: 19368888  |  Reference-DOI: 10.1016/J.STR.2009.02.008

(-) Compounds

Molecule 1 - EXCINUCLEASE ABC, SUBUNIT A.
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PLX02
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: RESIDUES 81-922
    Mutation: YES
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 1299
    Synonym: UVRA2

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): AB 
Biological Unit 2 (2x):   C
Biological Unit 3 (1x): A  
Biological Unit 4 (1x):  B 
Biological Unit 5 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1ADP6Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3ZN6Ligand/IonZINC ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1ADP4Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1ADP4Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3ZN-1Ligand/IonZINC ION
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3ZN-1Ligand/IonZINC ION
Biological Unit 5 (1, 2)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:24 , ASN A:25 , VAL A:44 , GLY A:46 , SER A:47 , GLY A:48 , LYS A:49 , SER A:50 , SER A:51 , ARG A:101 , GLN A:726 , GLU A:730 , HOH A:1066 , HOH A:1045 , HOH A:1001 , HOH A:1063 , HOH A:1098 , HOH A:1088BINDING SITE FOR RESIDUE ADP A 1843
02AC2SOFTWARETYR A:370 , ARG A:375 , ASN A:511 , ASN A:512 , VAL A:531 , GLY A:533 , SER A:534 , GLY A:535 , LYS A:536 , SER A:537 , THR A:538 , GLY A:810BINDING SITE FOR RESIDUE ADP A 1842
03AC3SOFTWAREHIS B:24 , ASN B:25 , VAL B:44 , GLY B:46 , SER B:47 , GLY B:48 , LYS B:49 , SER B:50 , SER B:51 , ARG B:101 , GLN B:726 , GLU B:730 , HOH B:1002 , HOH B:1028BINDING SITE FOR RESIDUE ADP B 1843
04AC4SOFTWARETYR B:370 , ARG B:375 , ASN B:511 , ASN B:512 , VAL B:531 , GLY B:533 , SER B:534 , GLY B:535 , LYS B:536 , SER B:537 , THR B:538 , HOH B:1113 , HOH B:1037 , HOH B:1137BINDING SITE FOR RESIDUE ADP B 1842
05AC5SOFTWAREHIS C:24 , ASN C:25 , VAL C:44 , SER C:45 , GLY C:46 , SER C:47 , GLY C:48 , LYS C:49 , SER C:50 , SER C:51 , ARG C:101 , LEU C:722 , GLN C:726 , GLU C:730 , MG C:905 , HOH C:1034 , HOH C:1116 , HOH C:1019BINDING SITE FOR RESIDUE ADP C 1843
06AC6SOFTWARETYR C:370 , ARG C:375 , ASN C:511 , ASN C:512 , SER C:532 , GLY C:533 , SER C:534 , GLY C:535 , LYS C:536 , SER C:537 , THR C:538 , GLY C:810 , HOH C:1012 , HOH C:1007 , HOH C:1040 , HOH C:1025BINDING SITE FOR RESIDUE ADP C 1842
07AC7SOFTWARECYS A:151 , CYS A:154 , CYS A:287 , CYS A:290BINDING SITE FOR RESIDUE ZN A 1844
08AC8SOFTWARECYS A:641 , CYS A:644 , CYS A:664 , CYS A:667BINDING SITE FOR RESIDUE ZN A 1845
09AC9SOFTWARECYS B:151 , CYS B:154 , CYS B:287 , CYS B:290BINDING SITE FOR RESIDUE ZN B 1844
10BC1SOFTWARECYS B:641 , CYS B:644 , CYS B:664 , CYS B:667BINDING SITE FOR RESIDUE ZN B 1845
11BC2SOFTWARECYS C:151 , CYS C:154 , CYS C:287 , CYS C:290BINDING SITE FOR RESIDUE ZN C 1844
12BC3SOFTWARECYS C:641 , CYS C:644 , CYS C:664 , CYS C:667BINDING SITE FOR RESIDUE ZN C 1845
13BC4SOFTWAREARG C:101 , GLU C:735 , ADP C:902BINDING SITE FOR RESIDUE MG C 1846

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VF7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2VF7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VF7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VF7)

(-) Exons   (0, 0)

(no "Exon" information available for 2VF7)

(-) 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:815
 aligned with Q9RYW8_DEIRA | Q9RYW8 from UniProtKB/TrEMBL  Length:922

    Alignment length:832
                                   100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920  
         Q9RYW8_DEIRA    91 PDGGFVQVRGARQHNLKDISVKVPRDALVVFTGVSGSGKSSLAFGTLYAEAQRRYLESVSPYARRLFNQAGVPDVDAIDGLPPAVALQQARGTPTARSSVGSVTTLSNLLRMLYSRAGDYPPGQGIVYAEGFSPNTPEGACPECHGLGRVYTVTEDSMVPDPSLTIRERAVAAWPQAWGGQNQRDILVTLGIDVDVPWRELPEETRHWILFTDEQPVVPVYPGLTPAETQRALKKKMEPSYMGTFSSARRHVLHTFANTESASMKKRVQGYMISEECPLCHGKRLRQEALNVTFAGLDITELSRLPLARVSELLRPYAEEREPGHAERVKNRPEQAIALQRMAADLVKRLDVLLHLGLGYLGLDRSTPTLSPGELQRLRLATQLYSNLFGVVYVLDEPSAGLHPADTEALLSALENLKRGGNSLFVVEHDLDVIRRADWLVDVGPEAGEKGGEILYSGPPEGLKHVPESQTGQYLFADRHTEPHTPREPAGWLELNGVTRNNLDNLDVRFPLGVMTSVTGVSGSGKSTLVSQALVDALAAHFGQPVNPDPEDDEDPADHTAGSARLGGDLAQITRLVRVDQKPIGRTPRSNMATYTGLFDQVRKLFAATPLAKKRGYNAGRFSFNVKGGRCEHCQGEGWVMVELLFLPSVYAPCPVCHGTRYNAETLEVEYRGKNIADVLALTVDEAHDFFADESAIFRALDTLREVGLGYLRLGQPATELSGGEAQRIKLATELQRSGRGGTVYVLDEPTTGLHPADVERLQRQLVKLVDAGNTVIAVEHKMQVVAASDWVLDIGPGAGEDGGRLVAQGTPAEVAQAAGSVTAPYLRAALR 922
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.......eeeeee...eeeee.....hhhhhhh.hhhhhhhhhhhhhhh.....hhhhhh.....eee....eee............hhhhhhhhhhhhhhhhhhhh.........hhhhhh...............eeee.hhhhhh................hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhh....eeee..hhhhhhhhhhhhh.hhhhhhhhhhhheeee.....................hhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.......eeeee......hhhhhhhhhhhhhhhhh...eeeee..hhhhhh...eeeee...hhhhh..eeeeehhhhhhhh..hhhhhhhhh..............eeeeeeeee..eeeeeeeee...eeeee.....hhhhhh...hhhhhhhhh..-----------------...eeee.hhhh.eeeee...........hhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhh...............eeee.......eeee...........hhhhh.....hhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh........eeeeee......hhhhhhhhhhhhhhhhhh..eeeee..hhhhhh...eeeee...hhhhh..eeeeehhhhhh......hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vf7 A  11 PDGGFVQVRGARQHNLKDISVKVPRDALVVFTGVSGSGKSSLAFGTLYAEAQRRYLESVSPYARRLFNQAGVPDVDAIDGLPPAVALQQARGTPTARSSVGSVTTLSNLLRMLYSRAGDYPPGQGIVYAEGFSPNTPEGACPECHGLGRVYTVTEDSMVPDPSLTIRERAVAAWPQAWGGQNQRDILVTLGIDVDVPWRELPEETRHWILFTDEQPVVPVYPGLTPAETQRALKKKMEPSYMGTFSSARRHVLHTFANTESASMKKRVQGYMISEECPLCHGKRLRQEALNVTFAGLDITELSRLPLARVSELLRPYAEEREPGHAERVKNRPEQAIALQRMAADLVKRLDVLLHLGLGYLGLDRSTPTLSPGELQRLRLATQLYSNLFGVVYVLDEPSAGLHPADTEALLSALENLKRGGNSLFVVEHDLDVIRRADWLVDVGPEAGEKGGEILYSGPPEGLKHVPESQTGQYLFADRHTEPHTPREPAGWLELNGVTRNNLDNLDVRFPLGVMTSVTGVSGSGKSTLVSQALVDALAAHFGQ-----------------GSARLGGDLAQITRLVRVDQKPIGRTPRSNMATYTGLFDQVRKLFAATPLAKKRGYNAGRFSFNVKGGRCEHCQGEGWVMVELLFLPSVYAPCPVCHGTRYNAETLEVEYRGKNIADVLALTVDEAHDFFADESAIFRALDTLREVGLGYLRLGQPATELSGGEAQRIKLATELRRSGRGGTVYVLDEPTTGLHPADVERLQRQLVKLVDAGNTVIAVEHKMQVVAASDWVLDIGPGAGEDGGRLVAQGTPAEVAQAAGSVTAPYLRAALR 842
                                    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       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550   |     -         - |     580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         554               572                                                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:813
 aligned with Q9RYW8_DEIRA | Q9RYW8 from UniProtKB/TrEMBL  Length:922

    Alignment length:835
                                    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       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887       897       907       917     
         Q9RYW8_DEIRA    88 PDFPDGGFVQVRGARQHNLKDISVKVPRDALVVFTGVSGSGKSSLAFGTLYAEAQRRYLESVSPYARRLFNQAGVPDVDAIDGLPPAVALQQARGTPTARSSVGSVTTLSNLLRMLYSRAGDYPPGQGIVYAEGFSPNTPEGACPECHGLGRVYTVTEDSMVPDPSLTIRERAVAAWPQAWGGQNQRDILVTLGIDVDVPWRELPEETRHWILFTDEQPVVPVYPGLTPAETQRALKKKMEPSYMGTFSSARRHVLHTFANTESASMKKRVQGYMISEECPLCHGKRLRQEALNVTFAGLDITELSRLPLARVSELLRPYAEEREPGHAERVKNRPEQAIALQRMAADLVKRLDVLLHLGLGYLGLDRSTPTLSPGELQRLRLATQLYSNLFGVVYVLDEPSAGLHPADTEALLSALENLKRGGNSLFVVEHDLDVIRRADWLVDVGPEAGEKGGEILYSGPPEGLKHVPESQTGQYLFADRHTEPHTPREPAGWLELNGVTRNNLDNLDVRFPLGVMTSVTGVSGSGKSTLVSQALVDALAAHFGQPVNPDPEDDEDPADHTAGSARLGGDLAQITRLVRVDQKPIGRTPRSNMATYTGLFDQVRKLFAATPLAKKRGYNAGRFSFNVKGGRCEHCQGEGWVMVELLFLPSVYAPCPVCHGTRYNAETLEVEYRGKNIADVLALTVDEAHDFFADESAIFRALDTLREVGLGYLRLGQPATELSGGEAQRIKLATELQRSGRGGTVYVLDEPTTGLHPADVERLQRQLVKLVDAGNTVIAVEHKMQVVAASDWVLDIGPGAGEDGGRLVAQGTPAEVAQAAGSVTAPYLRAALR 922
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeee.......eeeeee...eeeeee....hhhhhhh.hhhhhhhhhhhhhhh................eee....eee............hhhhhhhhhhhhhhhhhhh..........hhhhhh...............eeee.hhhhhh.................hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhh.....eeee..hhhhhhhhhhhhh.hhhhhhhhhh..eeee.........hhhhhh......hhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.......eeeee.........hhhhhhhhhhhhhh...eeeee..hhhhhhhh.eeeee...hhhhh..eeeeehhhhhhh...hhhhhhhhh.............eeeeeeeeee..eeeeeeeeee..eeeeee....hhhhhhhhhhhhhhhhhh..-----------------.eeee..hhhhh.eeeee...........hhhhhhhhhhhhhhhh...hhhhhh.......................eee.-----...eee...........hhhhh.....hhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhhh........hhhhh.hhhhhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhhhhh..eeeee..hhhhhh...eeeee...hhhhh..eeeeehhhhhhh.....hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vf7 B   8 PDFPDGGFVQVRGARQHNLKDISVKVPRDALVVFTGVSGSGKSSLAFGTLYAEAQRRYLESVSPYARRLFNQAGVPDVDAIDGLPPAVALQQARGTPTARSSVGSVTTLSNLLRMLYSRAGDYPPGQGIVYAEGFSPNTPEGACPECHGLGRVYTVTEDSMVPDPSLTIRERAVAAWPQAWGGQNQRDILVTLGIDVDVPWRELPEETRHWILFTDEQPVVPVYPGLTPAETQRALKKKMEPSYMGTFSSARRHVLHTFANTESASMKKRVQGYMISEECPLCHGKRLRQEALNVTFAGLDITELSRLPLARVSELLRPYAEEREPGHAERVKNRPEQAIALQRMAADLVKRLDVLLHLGLGYLGLDRSTPTLSPGELQRLRLATQLYSNLFGVVYVLDEPSAGLHPADTEALLSALENLKRGGNSLFVVEHDLDVIRRADWLVDVGPEAGEKGGEILYSGPPEGLKHVPESQTGQYLFADRHTEPHTPREPAGWLELNGVTRNNLDNLDVRFPLGVMTSVTGVSGSGKSTLVSQALVDALAAHFGQ-----------------GSARLGGDLAQITRLVRVDQKPIGRTPRSNMATYTGLFDQVRKLFAATPLAKKRGYNAGRFSFNVKGGRCEHCQGEGWVMV-----PSVYAPCPVCHGTRYNAETLEVEYRGKNIADVLALTVDEAHDFFADESAIFRALDTLREVGLGYLRLGQPATELSGGEAQRIKLATELRRSGRGGTVYVLDEPTTGLHPADVERLQRQLVKLVDAGNTVIAVEHKMQVVAASDWVLDIGPGAGEDGGRLVAQGTPAEVAQAAGSVTAPYLRAALR 842
                                    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       447       457       467       477       487       497       507       517       527       537       547      |  -         -    |  577       587       597       607       617       627       637       647    |    -|      667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            554               572                                                                             652   658                                                                                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:814
 aligned with Q9RYW8_DEIRA | Q9RYW8 from UniProtKB/TrEMBL  Length:922

    Alignment length:833
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869       879       889       899       909       919   
         Q9RYW8_DEIRA    90 FPDGGFVQVRGARQHNLKDISVKVPRDALVVFTGVSGSGKSSLAFGTLYAEAQRRYLESVSPYARRLFNQAGVPDVDAIDGLPPAVALQQARGTPTARSSVGSVTTLSNLLRMLYSRAGDYPPGQGIVYAEGFSPNTPEGACPECHGLGRVYTVTEDSMVPDPSLTIRERAVAAWPQAWGGQNQRDILVTLGIDVDVPWRELPEETRHWILFTDEQPVVPVYPGLTPAETQRALKKKMEPSYMGTFSSARRHVLHTFANTESASMKKRVQGYMISEECPLCHGKRLRQEALNVTFAGLDITELSRLPLARVSELLRPYAEEREPGHAERVKNRPEQAIALQRMAADLVKRLDVLLHLGLGYLGLDRSTPTLSPGELQRLRLATQLYSNLFGVVYVLDEPSAGLHPADTEALLSALENLKRGGNSLFVVEHDLDVIRRADWLVDVGPEAGEKGGEILYSGPPEGLKHVPESQTGQYLFADRHTEPHTPREPAGWLELNGVTRNNLDNLDVRFPLGVMTSVTGVSGSGKSTLVSQALVDALAAHFGQPVNPDPEDDEDPADHTAGSARLGGDLAQITRLVRVDQKPIGRTPRSNMATYTGLFDQVRKLFAATPLAKKRGYNAGRFSFNVKGGRCEHCQGEGWVMVELLFLPSVYAPCPVCHGTRYNAETLEVEYRGKNIADVLALTVDEAHDFFADESAIFRALDTLREVGLGYLRLGQPATELSGGEAQRIKLATELQRSGRGGTVYVLDEPTTGLHPADVERLQRQLVKLVDAGNTVIAVEHKMQVVAASDWVLDIGPGAGEDGGRLVAQGTPAEVAQAAGSVTAPYLRAALR 922
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ABC_tran-2vf7C01 C:572-762                                                                                                                                                                     -------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ABC_tran-2vf7C02 C:572-762                                                                                                                                                                     -------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ABC_tran-2vf7C03 C:572-762                                                                                                                                                                     -------------------------------------------------------------------------------- Pfam domains (3)
         Sec.struct. author .....eeeeeee.......eeeeee...eeeee.....hhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhh.....eee....eee............hhhhhhhhhhhhhhhhhhh...............................eeee.hhhhhh.................hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhh.....eeee..hhhhhhhhhhhhh...hhhhhhhh..eeee.........hhhhhh......hhhhhhh.hhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.......eeeee......hhhhhhhhhhhhhhhhh...eeeee..hhhhhh...eeeee...hhhhh..eeeeehhhhhhhh..hhhhhhhhh.............eeeeeeeeee..eeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhh-------------------...eeee......eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh...............eee.........eee.........hhhhhh.ee..eehhhhhh.hhhhhhhhh..hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh...hhhhh.eeeeee......hhhhhhhhhhhhhhhhhh..eeeee..hhhhhh...eeeee..........eeeeehhhhhh......hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vf7 C  10 FPDGGFVQVRGARQHNLKDISVKVPRDALVVFTGVSGSGKSSLAFGTLYAEAQRRYLESVSPYARRLFNQAGVPDVDAIDGLPPAVALQQARGTPTARSSVGSVTTLSNLLRMLYSRAGDYPPGQGIVYAEGFSPNTPEGACPECHGLGRVYTVTEDSMVPDPSLTIRERAVAAWPQAWGGQNQRDILVTLGIDVDVPWRELPEETRHWILFTDEQPVVPVYPGLTPAETQRALKKKMEPSYMGTFSSARRHVLHTFANTESASMKKRVQGYMISEECPLCHGKRLRQEALNVTFAGLDITELSRLPLARVSELLRPYAEEREPGHAERVKNRPEQAIALQRMAADLVKRLDVLLHLGLGYLGLDRSTPTLSPGELQRLRLATQLYSNLFGVVYVLDEPSAGLHPADTEALLSALENLKRGGNSLFVVEHDLDVIRRADWLVDVGPEAGEKGGEILYSGPPEGLKHVPESQTGQYLFADRHTEPHTPREPAGWLELNGVTRNNLDNLDVRFPLGVMTSVTGVSGSGKSTLVSQALVDALAAHF-------------------GSARLGGDLAQITRLVRVDQKPIGRTPRSNMATYTGLFDQVRKLFAATPLAKKRGYNAGRFSFNVKGGRCEHCQGEGWVMVELLFLPSVYAPCPVCHGTRYNAETLEVEYRGKNIADVLALTVDEAHDFFADESAIFRALDTLREVGLGYLRLGQPATELSGGEAQRIKLATELRRSGRGGTVYVLDEPTTGLHPADVERLQRQLVKLVDAGNTVIAVEHKMQVVAASDWVLDIGPGAGEDGGRLVAQGTPAEVAQAAGSVTAPYLRAALR 842
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549  |      -         -  |    579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        552                 572
   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 2VF7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VF7)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q9RYW8_DEIRA | Q9RYW8)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0009381    excinuclease ABC activity    Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid at sites flanking regions of damaged DNA to which the Uvr ABC excinuclease complexes bind.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    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.
biological process
    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: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:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0006289    nucleotide-excision repair    A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0009380    excinuclease repair complex    Any of the protein complexes formed by the UvrABC excinuclease system, which carries out nucleotide excision repair. Three different complexes are formed by the 3 proteins as they proceed through the excision repair process. First a complex consisting of two A subunits and two B subunits bind DNA and unwind it around the damaged site. Then, the A subunits disassociate leaving behind a stable complex between B subunits and DNA. Now, subunit C binds to this B+DNA complex and causes subunit B to nick the DNA on one side of the complex while subunit C nicks the DNA on the other side of the complex. DNA polymerase I and DNA ligase can then repair the resulting gap.

 Visualization

(-) Interactive Views

Asymmetric 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
    ADP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2vf7)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]
    Biological Unit 5  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 PNG format | Biol. Unit 5 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
  2vf7
    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
  Q9RYW8_DEIRA | Q9RYW8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  Q9RYW8_DEIRA | Q9RYW8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9RYW8_DEIRA | Q9RYW8: 2vf8

(-) Related Entries Specified in the PDB File

2vf8 CRYSTAL STRUCTURE OF UVRA2 FROM DEINOCOCCUS RADIODURANS