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(-) Description

Title :  STRUCTURE OF AN ENTEROCOCCUS FAECALIS HD-DOMAIN PROTEIN COMPLEXED WITH DGTP AND DTTP
 
Authors :  I. I. Vorontsov, G. Minasov, L. Shuvalova, A. Joachimiak, W. F. Anderso Center For Structural Genomics (Mcsg)
Date :  19 Jul 13  (Deposition) - 20 Nov 13  (Release) - 12 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  C,D  (1x)
Keywords :  Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Hd Domain, Phosphohydrolase, Dntpase, Allosteric Regulation, Metal Binding Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. I. Vorontsov, Y. Wu, M. Delucia, G. Minasov, J. Mehrens, L. Shuvalova, W. F. Anderson, J. Ahn
Mechanisms Of Allosteric Activation And Inhibition Of The Deoxyribonucleoside Triphosphate Triphosphohydrolase From Enterococcus Faecalis.
J. Biol. Chem. V. 289 2815 2014
PubMed-ID: 24338016  |  Reference-DOI: 10.1074/JBC.M113.524207

(-) Compounds

Molecule 1 - HD DOMAIN PROTEIN
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMCSG7
    Expression System StrainBL21-DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneEF-1143, EF_1143
    Organism ScientificENTEROCOCCUS FAECALIS
    Organism Taxid226185
    StrainV583

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)ABCD
Biological Unit 2 (1x)AB  
Biological Unit 3 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 15)

Asymmetric Unit (5, 15)
No.NameCountTypeFull Name
1DGT4Ligand/Ion2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
2MLI2Ligand/IonMALONATE ION
3NI4Ligand/IonNICKEL (II) ION
4TRS3Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
5TTP2Ligand/IonTHYMIDINE-5'-TRIPHOSPHATE
Biological Unit 1 (4, 11)
No.NameCountTypeFull Name
1DGT4Ligand/Ion2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
2MLI2Ligand/IonMALONATE ION
3NI-1Ligand/IonNICKEL (II) ION
4TRS3Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
5TTP2Ligand/IonTHYMIDINE-5'-TRIPHOSPHATE
Biological Unit 2 (4, 7)
No.NameCountTypeFull Name
1DGT2Ligand/Ion2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
2MLI1Ligand/IonMALONATE ION
3NI-1Ligand/IonNICKEL (II) ION
4TRS3Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
5TTP1Ligand/IonTHYMIDINE-5'-TRIPHOSPHATE
Biological Unit 3 (3, 4)
No.NameCountTypeFull Name
1DGT2Ligand/Ion2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
2MLI1Ligand/IonMALONATE ION
3NI-1Ligand/IonNICKEL (II) ION
4TRS-1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
5TTP1Ligand/IonTHYMIDINE-5'-TRIPHOSPHATE

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:66 , HIS A:110 , ASP A:111 , ASP A:183 , HOH A:651 , HOH A:801BINDING SITE FOR RESIDUE NI A 501
02AC2SOFTWARELYS A:14 , VAL A:15 , PHE A:16 , ILE A:35 , ASN A:36 , GLN A:41 , ARG A:44 , PHE A:64 , HOH A:841 , PHE B:54 , THR B:55 , ARG B:326 , LYS B:330 , HOH B:729 , HOH B:737 , HOH B:780BINDING SITE FOR RESIDUE DGT A 502
03AC3SOFTWAREASP A:318 , ARG A:322 , PHE A:356 , TYR A:361 , HOH A:796BINDING SITE FOR RESIDUE TRS A 503
04AC4SOFTWAREHIS B:66 , HIS B:110 , ASP B:111 , ASP B:183 , HOH B:742 , HOH B:786BINDING SITE FOR RESIDUE NI B 501
05AC5SOFTWAREPHE A:54 , THR A:55 , VAL A:247 , ARG A:326 , LYS A:330 , HOH A:677 , LYS B:14 , VAL B:15 , PHE B:16 , ASN B:36 , GLN B:41 , ARG B:44 , PHE B:64 , TTP B:503 , HOH B:749BINDING SITE FOR RESIDUE DGT B 502
06AC6SOFTWARETHR A:55 , PHE A:56 , GLN A:241 , HIS A:245 , HOH A:630 , HOH A:652 , HOH A:677 , HOH A:729 , HOH A:764 , HOH A:815 , VAL B:15 , ARG B:17 , DGT B:502 , ARG D:206 , ARG D:209 , ASN D:223 , HOH D:702BINDING SITE FOR RESIDUE TTP B 503
07AC7SOFTWAREGLU B:7BINDING SITE FOR RESIDUE MLI B 504
08AC8SOFTWAREASP B:318 , PHE B:356 , HOH B:787BINDING SITE FOR RESIDUE TRS B 505
09AC9SOFTWAREGLN B:135 , PHE B:288BINDING SITE FOR RESIDUE TRS B 506
10BC1SOFTWAREHIS C:66 , HIS C:110 , ASP C:111 , ASP C:183 , HOH C:747 , HOH C:756BINDING SITE FOR RESIDUE NI C 501
11BC2SOFTWARELYS C:14 , VAL C:15 , PHE C:16 , ILE C:35 , ASN C:36 , GLN C:41 , ARG C:44 , PHE C:64 , PHE D:54 , THR D:55 , VAL D:247 , ARG D:326 , LYS D:330 , LYS D:422 , HOH D:675 , HOH D:716 , HOH D:718BINDING SITE FOR RESIDUE DGT C 502
12BC3SOFTWAREVAL C:354 , GLY C:355 , PHE C:356 , TYR C:361 , HOH C:730BINDING SITE FOR RESIDUE MLI C 503
13BC4SOFTWAREHIS D:66 , HIS D:110 , ASP D:111 , ASP D:183 , HOH D:698 , HOH D:725BINDING SITE FOR RESIDUE NI D 501
14BC5SOFTWAREPHE C:54 , THR C:55 , VAL C:247 , ARG C:326 , LYS C:330 , LYS C:422 , HOH C:713 , HOH C:724 , LYS D:14 , VAL D:15 , PHE D:16 , ASN D:36 , GLN D:41 , ARG D:44 , PHE D:64 , TTP D:503 , HOH D:601BINDING SITE FOR RESIDUE DGT D 502
15BC6SOFTWAREARG B:206 , ARG B:209 , HOH B:664 , THR C:55 , PHE C:56 , GLN C:241 , HIS C:245 , HOH C:641 , HOH C:699 , HOH C:711 , VAL D:15 , ARG D:17 , DGT D:502 , HOH D:601BINDING SITE FOR RESIDUE TTP D 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LRL)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4LRL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LRL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LRL)

(-) Exons   (0, 0)

(no "Exon" information available for 4LRL)

(-) 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:451
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4lrla_ A: Hypothetical protein EF1143                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhh.eeeeeeeeee...eeeeeeehhhhhhhhhhhhhhhhhh..hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh......hhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhh....hhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhheeee..eeeee..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhh...hhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhhhh..hhhhhheeee.hhh..........hhhhh.eee.....eeehhhhhhhhhhhhh.....eeeeehhhhh....hhhhhhhhhh.ee..ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lrl A   0 AMTIPYKEQRLPIEKVFRDPVHNYIHVQHQVILDLINSAEVQRLRRIKQLGTSSFTFHGAEHSRFSHSLGVYEITRRICEIFQRNYSVERLGENGWNDDERLITLCAALLHDVGHGPYSHTFEHIFDTNHEAITVQIITSPETEVYQILNRVSADFPEKVASVITKQYPNPQVVQMISSQIDADRMDYLLRDAYFTGTEYGTFDLTRILRVIRPYKGGIAFAMNGMHAVEDYIVSRYQMYVQVYFHPVSRGMEVILDHLLHRAKELFENPEFDYDLQASLLVPFFKGDFTLQEYLKLDDGVLSTYFTQWMDVPDSILGDLAKRFLMRKPLKSATFTNEKESAATIAYLRELIEKVGFNPKYYTAINSSYDLPYDFYRPNKDRHRTQIELMQKDGSLVELATVSPLVAALAGQSQGDERFYFPKEMLDQDLFDETYREFSSYIHNGALVLKK 456
                                     9        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       435       445       455 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                     427|                      
                                                                                                                                                                                                                                                                                                                                                                                                                                                                      434                      

Chain B from PDB  Type:PROTEIN  Length:445
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4lrlb_ B: Hypothetical protein EF1143                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhh.eeeeeeeeee...eeeeeeehhhhhhhhhhhhhhhhhh....hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......hhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhh....hhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhheeee..eeeee..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh............hhhhhh...hhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhh..hhhhhheeee.................eee.....eeehhhhhhhhhhhhh.....eeeeehhhhhh..hhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lrl B   2 TIPYKEQRLPIEKVFRDPVHNYIHVQHQVILDLINSAEVQRLRRIKQLGTSSFTFHGAEHSRFSHSLGVYEITRRICEIFQRNYSVERLGENGWNDDERLITLCAALLHDVGHGPYSHTFEHIFDTNHEAITVQIITSPETEVYQILNRVSADFPEKVASVITKQYPNPQVVQMISSQIDADRMDYLLRDAYFTGTEYGTFDLTRILRVIRPYKGGIAFAMNGMHAVEDYIVSRYQMYVQVYFHPVSRGMEVILDHLLHRAKELFENPEFDYDLQASLLVPFFKGDFTLQEYLKLDDGVLSTYFTQWMDVPDSILGDLAKRFLMRKPLKSATFTNEKESAATIAYLRELIEKVGFNPKYYTAINSSYDLPYDFYRPRHRTQIELMQKDGSLVELATVSPLVAALAGQSQGDERFYFPKEMLDDLFDETYREFSSYIHNGALVLKK 456
                                    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     ||384       394       404       414       424 ||    441       451     
                                                                                                                                                                                                                                                                                                                                                                                                                 377|                                          426|                      
                                                                                                                                                                                                                                                                                                                                                                                                                  381                                           434                      

Chain C from PDB  Type:PROTEIN  Length:455
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d4lrlc_ C: Hypothetical protein EF1143                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhh.eeeeeeeeee...eeeeeeehhhhhhhhhhhhhhhhhh..hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......hhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhh....hhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhheeee..eeeee..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhh...hhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhhhh..hhhhhheeehhhhh..........hhhhh.eee.....eeehhhhhhhhhhhhhh.....eeeehhhhh..........hhhhhhhhhh.ee..ee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lrl C   2 TIPYKEQRLPIEKVFRDPVHNYIHVQHQVILDLINSAEVQRLRRIKQLGTSSFTFHGAEHSRFSHSLGVYEITRRICEIFQRNYSVERLGENGWNDDERLITLCAALLHDVGHGPYSHTFEHIFDTNHEAITVQIITSPETEVYQILNRVSADFPEKVASVITKQYPNPQVVQMISSQIDADRMDYLLRDAYFTGTEYGTFDLTRILRVIRPYKGGIAFAMNGMHAVEDYIVSRYQMYVQVYFHPVSRGMEVILDHLLHRAKELFENPEFDYDLQASLLVPFFKGDFTLQEYLKLDDGVLSTYFTQWMDVPDSILGDLAKRFLMRKPLKSATFTNEKESAATIAYLRELIEKVGFNPKYYTAINSSYDLPYDFYRPNKDRHRTQIELMQKDGSLVELATVSPLVAALAGQSQGDERFYFPKEMLDQGNKKHYDLFDETYREFSSYIHNGALVLKK 456
                                    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     

Chain D from PDB  Type:PROTEIN  Length:439
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d4lrld_ D: Hypothetical protein EF1143                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhh.eeeeeeeeee...eeeeeeehhhhhhhhhhhhhhhhh.....hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......hhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhh....hhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhheeee..eeeee..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhh..hhhhhh..hhhhhhhhhhhhh...hhhhhhhhhhhhh....eeee......hhhhhhhhhhhhhhhh.hhhhhheeehhhhh..........hhhhh.eee.....eeehhhhhhhhhhhhhh.....eeeehhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lrl D   1 MTIPYKEQRLPIEKVFRDPVHNYIHVQHQVILDLINSAEVQRLRRIKQLGTSSFTFHGAEHSRFSHSLGVYEITRRICEIFQRNYSVERLGENGWNDDERLITLCAALLHDVGHGPYSHTFEHIFDTNHEAITVQIITSPETEVYQILNRVSADFPEKVASVITKQYPNPQVVQMISSQIDADRMDYLLRDAYFTGTEYGTFDLTRILRVIRPYKGGIAFAMNGMHAVEDYIVSRYQMYVQVYFHPVSRGMEVILDHLLHRAKELFENPEFDYDLQASLLVPFFKGDFTLQEYLKLDDGVLSTYFTQWMDVPDSILGDLAKRFLMRKPLKSATFTNEKESAATIAYLRELIEKVGFNPKYYTAINSSYDLPYDFYRPNKDRHRTQIELMQKDGSLVELATVSPLVAALAGQSQGDERFYFPKEMLDLFDETYREFSSYI 447
                                    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       290       300       310       320       330       340       350       360       370       380       390       400       410       420     ||438         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                   426|            
                                                                                                                                                                                                                                                                                                                                                                                                                                                                    435            

   Legend:   → Mismatch (orange background)
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  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  (1, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LRL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LRL)

(-) Gene Ontology  (2, 2)

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 Related Entries

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

UniProtKB/TrEMBL
        Q836G9_ENTFA | Q836G92o6i 3irh

(-) Related Entries Specified in the PDB File

2o6i APO FORM
3irh COMPLEX WITH DGTP AND DATP RELATED ID: MCSG-APC28984 RELATED DB: TARGETTRACK