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(-) Description

Title :  CRYSTAL STRUCTURE OF T5FEN IN COMPLEX INTACT SUBSTRATE AND METAL IONS.
 
Authors :  F. A. Almalki, M. Feng, J. Zhang, S. E. Sedelnikova, J. B. Rafferty, J. R. P. J. Artymiuk
Date :  18 Jan 16  (Deposition) - 01 Jun 16  (Release) - 20 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.22
Chains :  Asym. Unit :  A,B,X,Y
Biol. Unit 1:  B,X,Y  (1x)
Biol. Unit 2:  A,X,Y  (1x)
Keywords :  Hydrolase, Enzyme-Dna Complex, Flap Endonuclease, Metalloenzyme. (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. A. Almalki, C. S. Flemming, J. Zhang, M. Feng, S. E. Sedelnikova, T. Ceska, J. B. Rafferty, J. R. Sayers, P. J. Artymiuk
Direct Observation Of Dna Threading In Flap Endonuclease Complexes.
Nat. Struct. Mol. Biol. V. 23 640 2016
PubMed-ID: 27273516  |  Reference-DOI: 10.1038/NSMB.3241

(-) Compounds

Molecule 1 - DNA (5'-D(*AP*AP*AP*AP*GP*CP*GP*TP*AP*CP*GP*C)-3')
    Chains: X, Y
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 2 - EXODEOXYRIBONUCLEASE
    Chains: A, B
    EC Number: 3.1.11.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PJONEX4
    Expression System Strain: M72
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 20-291
    Gene: D15
    Organism Scientific: ESCHERICHIA PHAGE T5
    Organism Taxid: 10726
    Other Details: CORRESPONDS TO RESIDUES 20-291 OF UNIPROT P06229 BUT WITH MUTATION D153K
    Synonym: 5'-EXONUCLEASE,T5FEN, D15 EXONUCLEASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABXY
Biological Unit 1 (1x):  BXY
Biological Unit 2 (1x): A XY

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2K1Ligand/IonPOTASSIUM ION
3MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2K-1Ligand/IonPOTASSIUM ION
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2K-1Ligand/IonPOTASSIUM ION
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH B:409 , HOH B:423 , HOH B:450 , DC Y:6 , HOH Y:207binding site for residue MG Y 101
2AC2SOFTWAREHOH B:462 , DG Y:7 , HOH Y:205 , HOH Y:208 , HOH Y:212 , HOH Y:218binding site for residue MG Y 102
3AC3SOFTWAREMET A:199 , VAL A:209 , DC Y:10 , HOH Y:211binding site for residue K Y 103
4AC4SOFTWAREASP B:87 , LYS B:280 , ASP B:284 , DA Y:1 , DA Y:3binding site for residue GOL B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5HNK)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:234 -Pro A:235
2Leu B:234 -Pro B:235

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5HNK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5HNK)

(-) Exons   (0, 0)

(no "Exon" information available for 5HNK)

(-) 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:272
                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.ee.....hhhhhhhhhhhhhhhhh.eeeee..hhhhhhhh...eeee......eehhhhhhhhhh..hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hnk A  20 RNLMIVDGTNLGFRFKHNNSKKPFASSYVSTIQSLAKSYSARTTIVLGDKGKSVFRLEHLPEYKGNRDEKYAQRTEEEKALDEQFFEYLKDAFELCKTTFPTFTIRGVEADDMAAYIVKLIGHLYDHVWLISTKGDWDTLLTDKVSRFSFTTRREYHLRDMYEHHNVDDVEQFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFGNVLDIIDQLPLPGKQKYIQNLNASEELLFRNLILVDLPTYCVDAIAAVGQDVLDKFTKDILEIAEQ 291
                                    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  


Chain B from PDB  Type:PROTEIN  Length:272
                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeehhhhhhhhh.......hhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhh.....hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...ee.....hhhhhhhhhhhhhhhhh..eeee..hhhhhhhh...eeee......eehhhhhhhhhh..hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hnk B  20 RNLMIVDGTNLGFRFKHNNSKKPFASSYVSTIQSLAKSYSARTTIVLGDKGKSVFRLEHLPEYKGNRDEKYAQRTEEEKALDEQFFEYLKDAFELCKTTFPTFTIRGVEADDMAAYIVKLIGHLYDHVWLISTKGDWDTLLTDKVSRFSFTTRREYHLRDMYEHHNVDDVEQFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFGNVLDIIDQLPLPGKQKYIQNLNASEELLFRNLILVDLPTYCVDAIAAVGQDVLDKFTKDILEIAEQ 291
                                    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  


Chain X from PDB  Type:DNA  Length:12
                                            
                 5hnk X   1 AAAAGCGTACGC  12
                                    10  


Chain Y from PDB  Type:DNA  Length:12
                                            
                 5hnk Y   1 AAAAGCGTACGC  12
                                    10
   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 5HNK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5HNK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5HNK)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)

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  5hnk
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  EXO5_BPT5 | P06229
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  3.1.11.3
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 Related Entries

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

UniProtKB/Swiss-Prot
        EXO5_BPT5 | P06229: 1exn 1j5f 1ut5 1ut8 1xo1 5hml 5hmm 5hp4

(-) Related Entries Specified in the PDB File

5hml SAME PROTEIN BUT WITHOUT BOUND DNA