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(-) Description

Title :  CRYSTAL STRUCTURE HP-NAP FROM STRAIN YS39 ZINC SOAKED (20MM)
 
Authors :  H. Yokoyama, O. Tsuruta, N. Akao, S. Fujii
Date :  26 Apr 12  (Deposition) - 27 Jun 12  (Release) - 27 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (12x)
Keywords :  Dodecamer, Four-Helix Bundle, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Yokoyama, O. Tsuruta, N. Akao, S. Fujii
Crystal Structure Of Helicobacter Pylori Neutrophil-Activating Protein With A Di-Nuclear Ferroxidase Center In A Zinc Or Cadmium-Bound Form
Biochem. Biophys. Res. Commun. V. 422 745 2012
PubMed-ID: 22618234  |  Reference-DOI: 10.1016/J.BBRC.2012.05.073
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NEUTROPHIL-ACTIVATING PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NAPA
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 210
    Strain: YS39

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (12x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2SO41Ligand/IonSULFATE ION
3ZN7Ligand/IonZINC ION
Biological Unit 1 (2, 24)
No.NameCountTypeFull Name
1EDO12Ligand/Ion1,2-ETHANEDIOL
2SO412Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:25 , TYR A:44 , ASP A:52 , GLU A:56 , ZN A:202 , HOH A:301BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWAREHIS A:37 , GLU A:56 , ZN A:201 , HOH A:301 , HOH A:302BINDING SITE FOR RESIDUE ZN A 202
3AC3SOFTWAREHOH A:304BINDING SITE FOR RESIDUE ZN A 203
4AC4SOFTWAREHIS A:9 , ASP A:13 , HIS A:101 , GLU A:105BINDING SITE FOR RESIDUE ZN A 204
5AC5SOFTWAREHIS A:64 , HOH A:305 , HOH A:306 , HOH A:307BINDING SITE FOR RESIDUE ZN A 205
6AC6SOFTWAREHIS A:87 , HOH A:308 , HOH A:309 , HOH A:310BINDING SITE FOR RESIDUE ZN A 206
7AC7SOFTWAREGLU A:41 , GLU A:45 , HOH A:311 , HOH A:312BINDING SITE FOR RESIDUE ZN A 207
8AC8SOFTWAREILE A:43 , GLY A:46 , MET A:50 , TYR A:99 , HOH A:329 , HOH A:364BINDING SITE FOR RESIDUE EDO A 208
9AC9SOFTWAREPHE A:4 , LYS A:8 , HIS A:63 , HIS A:64BINDING SITE FOR RESIDUE SO4 A 209

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EVB)

(-) 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:143
                                                                                                                                                                               
               SCOP domains d4evba_ A: Dodecameric ferritin homolog                                                                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4evb A   2 KTFEILKHLQADAIVLFMKVHNFHWNVKGTDFFNVHKATEEIYEGFADMFDDLAERIAQLGHHPLVTLSEALKLTRVKEETKTSFHSKDIFKEILEDYKHLEKEFKELSNTAEKEGDKVTVTYADDQLAKLQKSIWMLQAHLA 144
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141
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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, 1)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        G1UIZ3_HELPX | G1UIZ3: 3t9j 3ta8 4evc

(-) Related Entries Specified in the PDB File

3t9j THE SAME PROTEIN IN APO FORM.
3ta8 THE SAME PROTEIN IN IRON-LOADED FORM.
4evc
4evd
4eve