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(-) Description

Title :  STRUCTURES OF DHBN DOMAIN OF HUMAN BLM HELICASE
 
Authors :  J. Shi, W. -F. Chen, B. Zhang, S. -H. Fan, X. Ai, N. -N. Liu, S. Rety, X. -G. X
Date :  02 Dec 16  (Deposition) - 01 Mar 17  (Release) - 19 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.16
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Helicase Dimerization Alpha-Helix Motif, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Shi, W. F. Chen, B. Zhang, S. H. Fan, X. Ai, N. N. Liu, S. Rety, X. G. Xi
A Helical Bundle In The N-Terminal Domain Of The Blm Helicase Mediates Dimer And Potentially Hexamer Formation.
J. Biol. Chem. V. 292 5909 2017
PubMed-ID: 28228481  |  Reference-DOI: 10.1074/JBC.M116.761510

(-) Compounds

Molecule 1 - BLOOM SYNDROME PROTEIN
    Chains: A, B, C, D
    EC Number: 3.6.4.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B-SUMO
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 362-414
    Gene: BLM, RECQ2, RECQL3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DNA HELICASE,RECQ-LIKE TYPE 2,RECQ2,RECQ PROTEIN-LIKE 3

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 23)

Asymmetric Unit (2, 23)
No.NameCountTypeFull Name
1IOD20Ligand/IonIODIDE ION
2K3Ligand/IonPOTASSIUM ION
Biological Unit 1 (1, 9)
No.NameCountTypeFull Name
1IOD9Ligand/IonIODIDE ION
2K-1Ligand/IonPOTASSIUM ION
Biological Unit 2 (1, 11)
No.NameCountTypeFull Name
1IOD11Ligand/IonIODIDE ION
2K-1Ligand/IonPOTASSIUM ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:381binding site for residue IOD A 502
02AC2SOFTWAREASP A:395binding site for residue IOD A 503
03AC3SOFTWAREGLN A:370 , GLU A:377binding site for residue IOD A 504
04AC4SOFTWARELEU A:382binding site for residue IOD A 505
05AC5SOFTWAREGLU A:377 , ASP C:362 , HOH C:629binding site for residue K A 506
06AC6SOFTWAREILE A:386 , LYS A:390binding site for residue IOD B 501
07AC7SOFTWAREHIS B:374 , LYS B:381binding site for residue IOD B 502
08AC8SOFTWAREARG B:407 , HOH B:609 , HOH B:631binding site for residue IOD B 504
09AC9SOFTWARELYS C:390 , HOH C:605binding site for residue K C 501
10AD1SOFTWAREHIS A:378 , HOH B:626 , ASP C:362binding site for residue K C 502
11AD2SOFTWARELYS C:390 , ASP D:395binding site for residue IOD C 503
12AD3SOFTWAREGLU C:413binding site for residue IOD C 507
13AD4SOFTWAREASP C:388 , ASP C:389binding site for residue IOD C 508
14AD5SOFTWAREARG D:407 , HOH D:618binding site for residue IOD D 501
15AD6SOFTWAREHIS D:378binding site for residue IOD D 502
16AD7SOFTWAREGLU D:399 , GLN D:402 , GLN D:403binding site for residue IOD D 503
17AD8SOFTWAREGLN D:402binding site for residue IOD D 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5MK5)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:413 -Val A:414

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5MK5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5MK5)

(-) Exons   (0, 0)

(no "Exon" information available for 5MK5)

(-) 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:51
                                                                                   
               SCOP domains --------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------- Transcript
                 5mk5 A 364 RQISLQQQLIHVMEHICKLIDTIPDDKLKLLDCGNELLQQRNIRRKLLTEV 414
                                   373       383       393       403       413 


Chain B from PDB  Type:PROTEIN  Length:52
                                                                                    
               SCOP domains ---------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------- Transcript
                 5mk5 B 362 DARQISLQQQLIHVMEHICKLIDTIPDDKLKLLDCGNELLQQRNIRRKLLTE 413
                                   371       381       391       401       411  


Chain C from PDB  Type:PROTEIN  Length:52
                                                                                    
               SCOP domains ---------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh..hhhhhh...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------- Transcript
                 5mk5 C 362 DARQISLQQQLIHVMEHICKLIDTIPDDKLKLLDCGNELLQQRNIRRKLLTE 413
                                   371       381       391       401       411  


Chain D from PDB  Type:PROTEIN  Length:48
                                                                                
               SCOP domains ------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------ Transcript
                 5mk5 D 365 QISLQQQLIHVMEHICKLIDTIPDDKLKLLDCGNELLQQRNIRRKLLT 412
                                   374       384       394       404
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (0, 0)

(no "SCOP Domain" information available for 5MK5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5MK5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5MK5)

(-) Gene Ontology  (54, 54)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/Swiss-Prot
        BLM_HUMAN | P54132: 2kv2 2mh9 2rrd 3we2 3we3 4cdg 4cgz 4o3m 5lup

(-) Related Entries Specified in the PDB File

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