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

(-) Description

Title :  CRYSTAL STRUCTURE OF ESCHERICHIA COLI TRANSCRIPTION-REPAIR COUPLING FACTOR
 
Authors :  A. M. Deaconescu, S. A. Darst
Date :  09 Nov 05  (Deposition) - 28 Feb 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Mfd, Sf2 Atpase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. Deaconescu, A. L. Chambers, A. J. Smith, B. E. Nickels, A. Hochschild, N. J. Savery, S. A. Darst
Structural Basis For Bacterial Transcription-Coupled Dna Repair.
Cell(Cambridge, Mass. ) V. 124 507 2006
PubMed-ID: 16469698  |  Reference-DOI: 10.1016/J.CELL.2005.11.045
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSCRIPTION-REPAIR COUPLING FACTOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MFD
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: TRCF

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1EPE5Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1EPE3Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2SO41Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:658 , THR A:659 , LEU A:660 , ARG A:685 , HIS B:842BINDING SITE FOR RESIDUE SO4 A 1149
2AC2SOFTWAREARG A:395 , ARG A:411BINDING SITE FOR RESIDUE SO4 A 1150
3AC3SOFTWAREARG B:395 , ARG B:411BINDING SITE FOR RESIDUE SO4 B 1149
4AC4SOFTWAREHIS A:842 , THR B:658 , THR B:659 , LEU B:660 , ARG B:685 , THR B:710 , HIS B:711 , LYS B:712BINDING SITE FOR RESIDUE EPE B 1150
5AC5SOFTWAREHIS A:897 , ARG A:900 , LEU A:936 , GLU A:937 , ASP A:938 , LEU A:939 , GLY A:940 , ALA A:941 , GLY A:942 , PHE A:943 , HOH A:1166BINDING SITE FOR RESIDUE EPE A 1151
6AC6SOFTWAREHIS B:897 , ARG B:900 , LEU B:936 , GLU B:937 , ASP B:938 , LEU B:939 , GLY B:940 , ALA B:941 , GLY B:942 , PHE B:943BINDING SITE FOR RESIDUE EPE B 1151
7AC7SOFTWAREGLN A:459 , ARG A:462 , ARG A:782 , ARG A:905 , SER A:906 , HIS A:907BINDING SITE FOR RESIDUE EPE A 1152
8AC8SOFTWARESER B:461 , ARG B:782 , ARG B:905 , SER B:906 , HIS B:907BINDING SITE FOR RESIDUE EPE B 1152

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2EYQ)

(-) 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:1146
 aligned with MFD_ECOLI | P30958 from UniProtKB/Swiss-Prot  Length:1148

    Alignment length:1146
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961       971       981       991      1001      1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      
           MFD_ECOLI      2 PEQYRYTLPVKAGEQRLLGELTGAACATLVAEIAERHAGPVVLIAPDMQNALRLHDEISQFTDQMVMNLADWETLPYDSFSPHQDIISSRLSTLYQLPTMQRGVLIVPVNTLMQRVCPHSFLHGHALVMKKGQRLSRDALRTQLDSAGYRHVDQVMEHGEYATRGALLDLFPMGSELPYRLDFFDDEIDSLRVFDVDSQRTLEEVEAINLLPAHEFPTDKAAIELFRSQWRDTFEVKRDPEHIYQQVSKGTLPAGIEYWQPLFFSEPLPPLFSYFPANTLLVNTGDLETSAERFQADTLARFENRGVDPMRPLLPPQSLWLRVDELFSELKNWPRVQLKTEHLPTKAANANLGFQKLPDLAVQAQQKAPLDALRKFLETFDGPVVFSVESEGRREALGELLARIKIAPQRIMRLDEASDRGRYLMIGAAEHGFVDTVRNLALICESDLLGERVARRRQDSRRTINPDTLIRNLAELHIGQPVVHLEHGVGRYAGMTTLEAGGITGEYLMLTYANDAKLYVPVSSLHLISRYAGGAEENAPLHKLGGDAWSRARQKAAEKVRDVAAELLDIYAQRAAKEGFAFKHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLLIVDEEHRFGVRHKERIKAMRANVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDSMVVREAILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFALATHDLEIRGAGELLGEEQSGSMETIGFSLYMELLENAVDALKAGREPSLEDLTSQQTEVELRMPSLLPDDFIPDVNTRLSFYKRIASAKTENELEEIKVELIDRFGLLPDPARTLLDIARLRQQAQKLGIRKLEGNEKGGVIEFAEKNHVNPAWLIGLLQKQPQHYRLDGPTRLKFIQDLSERKTRIEWVRQFMRELEENAI 1147
               SCOP domains d2eyqa4 A:2-348 Transcription-repair coupling factor, TRCF                                                                                                                                                                                                                                                                                                 d2eyqa2 A:349-465 Transcription-repair coupling factor, TRCF                                                         d2eyqa1 A:466-545 Transcription-repair coupling factor, RRCF, middle domain     d2eyqa3 A:546-778 Transcription-repair coupling factor, TRCF                                                                                                                                                                             d2eyqa5 A:779-989 Transcription-repair coupling factor, TRCF                                                                                                                                                       d2eyqa6 A:990-1147 Transcription-repair coupling factor, TRCF, C-terminal domain                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......................hhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh...eee..............hhhhhhhhhhhhhhhhhh..eeeeeehhhhh....hhhhhhhh.eeee.....hhhhhhhhhhhhh.eee.......eeeee..eeee........ee..ee..ee..eeee......eeeee.eeee........hhhhhhhhhhhhhhhh.......hhhhhhhh.....hhhhhhhhhh.....hhhhhh....eeeee.hhhhhhhhhhhhhhhhhhhh.........hhhhhh.hhhhhhhhhh...eeee...............ee..............hhhhhhhhh.......eee.hhhhhhhhhhhhhhhh...ee..hhhhh.....eeee......eee....eeeeehhhhh.........hhhhh.hhhhhhhh........eeee...eeeeeeeeeeee....eeeeeeee.hhh.eeeee.hhhh.eee................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....eeeee.......hhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhh....eeee.hhhhhh......eeeeeee.hhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhh...eeee..........eeeeeee.hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhh....eee.....hhhhhhhhhhhhhh....eeee...hhhhh....eeeeee......hhhhhhhhhh........eeeeeee.hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh.....ee.............hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...eee...eeeee.......hhhhhhhhhhhh...eeee...eeeee....hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2eyq A    2 PEQYRYTLPVKAGEQRLLGELTGAACATLVAEIAERHAGPVVLIAPDMQNALRLHDEISQFTDQMVMNLADWETLPYDSFSPHQDIISSRLSTLYQLPTMQRGVLIVPVNTLMQRVCPHSFLHGHALVMKKGQRLSRDALRTQLDSAGYRHVDQVMEHGEYATRGALLDLFPMGSELPYRLDFFDDEIDSLRVFDVDSQRTLEEVEAINLLPAHEFPTDKAAIELFRSQWRDTFEVKRDPEHIYQQVSKGTLPAGIEYWQPLFFSEPLPPLFSYFPANTLLVNTGDLETSAERFQADTLARFENRGVDPMRPLLPPQSLWLRVDELFSELKNWPRVQLKTEHLPTKAANANLGFQKLPDLAVQAQQKAPLDALRKFLETFDGPVVFSVESEGRREALGELLARIKIAPQRIMRLDEASDRGRYLMIGAAEHGFVDTVRNLALICESDLLGERVARRRQDSRRTINPDTLIRNLAELHIGQPVVHLEHGVGRYAGMTTLEAGGITGEYLMLTYANDAKLYVPVSSLHLISRYAGGAEENAPLHKLGGDAWSRARQKAAEKVRDVAAELLDIYAQRAAKEGFAFKHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLLIVDEEHRFGVRHKERIKAMRANVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDSMVVREAILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFALATHDLEIRGAGELLGEEQSGSMETIGFSLYMELLENAVDALKAGREPSLEDLTSQQTEVELRMPSLLPDDFIPDVNTRLSFYKRIASAKTENELEEIKVELIDRFGLLPDPARTLLDIARLRQQAQKLGIRKLEGNEKGGVIEFAEKNHVNPAWLIGLLQKQPQHYRLDGPTRLKFIQDLSERKTRIEWVRQFMRELEENAI 1147
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961       971       981       991      1001      1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      


Chain B from PDB  Type:PROTEIN  Length:1143
 aligned with MFD_ECOLI | P30958 from UniProtKB/Swiss-Prot  Length:1148

    Alignment length:1143
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144   
           MFD_ECOLI      5 YRYTLPVKAGEQRLLGELTGAACATLVAEIAERHAGPVVLIAPDMQNALRLHDEISQFTDQMVMNLADWETLPYDSFSPHQDIISSRLSTLYQLPTMQRGVLIVPVNTLMQRVCPHSFLHGHALVMKKGQRLSRDALRTQLDSAGYRHVDQVMEHGEYATRGALLDLFPMGSELPYRLDFFDDEIDSLRVFDVDSQRTLEEVEAINLLPAHEFPTDKAAIELFRSQWRDTFEVKRDPEHIYQQVSKGTLPAGIEYWQPLFFSEPLPPLFSYFPANTLLVNTGDLETSAERFQADTLARFENRGVDPMRPLLPPQSLWLRVDELFSELKNWPRVQLKTEHLPTKAANANLGFQKLPDLAVQAQQKAPLDALRKFLETFDGPVVFSVESEGRREALGELLARIKIAPQRIMRLDEASDRGRYLMIGAAEHGFVDTVRNLALICESDLLGERVARRRQDSRRTINPDTLIRNLAELHIGQPVVHLEHGVGRYAGMTTLEAGGITGEYLMLTYANDAKLYVPVSSLHLISRYAGGAEENAPLHKLGGDAWSRARQKAAEKVRDVAAELLDIYAQRAAKEGFAFKHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLLIVDEEHRFGVRHKERIKAMRANVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDSMVVREAILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFALATHDLEIRGAGELLGEEQSGSMETIGFSLYMELLENAVDALKAGREPSLEDLTSQQTEVELRMPSLLPDDFIPDVNTRLSFYKRIASAKTENELEEIKVELIDRFGLLPDPARTLLDIARLRQQAQKLGIRKLEGNEKGGVIEFAEKNHVNPAWLIGLLQKQPQHYRLDGPTRLKFIQDLSERKTRIEWVRQFMRELEENAI 1147
               SCOP domains d2eyqb4 B:5-348 Transcription-repair coupling factor, TRCF                                                                                                                                                                                                                                                                                              d2eyqb2 B:349-465 Transcription-repair coupling factor, TRCF                                                         d2eyqb1 B:466-545 Transcription-repair coupling factor, RRCF, middle domain     d2eyqb3 B:546-778 Transcription-repair coupling factor, TRCF                                                                                                                                                                             d2eyqb5 B:779-989 Transcription-repair coupling factor, TRCF                                                                                                                                                       d2eyqb6 B:990-1147 Transcription-repair coupling factor, TRCF, C-terminal domain                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................hhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh...eee..............hhhhhhhhhhhhhhh.....eeeeeehhhhh....hhhhhh...eeee.....hhhhhhhhhhhh..eee.......eeeee..eeee........eeeee....eeeeeee......eeeee.eeee........hhhhhhhhhhhhhh.........hhhhhhhh.....hhhhhhhhhh.....hhhhhh....eeee..hhhhhhhhhhhhhhhhhhhhh...............hhhhhhhh........................ee..............hhhhhhhhhhh...eeeee.hhhhhhhhhhhhh.....................eee......eee....eee......................hhhhhhh.........eeee...eeeeeeeeeeee....eeeeeeee.hhh.eeeee.hhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhhhhhhh....eeeee.......hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhh....eeee.hhhh........eeeeeee.hhhh.hhhhhhhhhhhh..eeeeee....hhhhhhhhh...eeee..........eeeeeee...hhhhhhhhhhhh....eeee.....hhhhhhhhhhh......eeee....hhhhhhhhhhhhhh....eeee...hhhhh......eeee......hhhhhhhhhhhh......eeeeeee.hhhhh..hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhh....................hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhheeeeeee..eeeeee......hhhhhhhhhhhh...eeee...eeeee....hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2eyq B    5 YRYTLPVKAGEQRLLGELTGAACATLVAEIAERHAGPVVLIAPDMQNALRLHDEISQFTDQMVMNLADWETLPYDSFSPHQDIISSRLSTLYQLPTMQRGVLIVPVNTLMQRVCPHSFLHGHALVMKKGQRLSRDALRTQLDSAGYRHVDQVMEHGEYATRGALLDLFPMGSELPYRLDFFDDEIDSLRVFDVDSQRTLEEVEAINLLPAHEFPTDKAAIELFRSQWRDTFEVKRDPEHIYQQVSKGTLPAGIEYWQPLFFSEPLPPLFSYFPANTLLVNTGDLETSAERFQADTLARFENRGVDPMRPLLPPQSLWLRVDELFSELKNWPRVQLKTEHLPTKAANANLGFQKLPDLAVQAQQKAPLDALRKFLETFDGPVVFSVESEGRREALGELLARIKIAPQRIMRLDEASDRGRYLMIGAAEHGFVDTVRNLALICESDLLGERVARRRQDSRRTINPDTLIRNLAELHIGQPVVHLEHGVGRYAGMTTLEAGGITGEYLMLTYANDAKLYVPVSSLHLISRYAGGAEENAPLHKLGGDAWSRARQKAAEKVRDVAAELLDIYAQRAAKEGFAFKHDREQYQLFCDSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQSDVKFKDLGLLIVDEEHRFGVRHKERIKAMRANVDILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDSMVVREAILREILRGGQVYYLYNDVENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWLLTPHPKAMTTDAQKRLEAIASLEDLGAGFALATHDLEIRGAGELLGEEQSGSMETIGFSLYMELLENAVDALKAGREPSLEDLTSQQTEVELRMPSLLPDDFIPDVNTRLSFYKRIASAKTENELEEIKVELIDRFGLLPDPARTLLDIARLRQQAQKLGIRKLEGNEKGGVIEFAEKNHVNPAWLIGLLQKQPQHYRLDGPTRLKFIQDLSERKTRIEWVRQFMRELEENAI 1147
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (3, 12)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MFD_ECOLI | P30958)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008026    ATP-dependent helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0015616    DNA translocase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive movement along a single- or double-stranded DNA molecule.
    GO:0043175    RNA polymerase core enzyme binding    Interacting selectively and non-covalently with an RNA polymerase core enzyme, containing a specific subunit composition defined as the core enzyme.
    GO:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    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:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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: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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0000716    transcription-coupled nucleotide-excision repair, DNA damage recognition    The identification of lesions on the actively transcribed strand of the DNA duplex as well as a small subset of lesions not recognized by the general nucleotide-excision repair pathway.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

 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
    EPE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2eyq)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 ](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
  2eyq
    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
  MFD_ECOLI | P30958
    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)
  (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
  MFD_ECOLI | P30958
    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
        MFD_ECOLI | P30958: 2b2n 3hjh 4dfc

(-) Related Entries Specified in the PDB File

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