Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
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 AN H-NOX PROTEIN FROM S. ONEIDENSIS IN THE FE(II) LIGATION STATE, Q154A/Q155A/K156A MUTANT
 
Authors :  M. A. Herzik Jr. , R. Jonnalagadda, J. Kuriyan, M. A. Marletta
Date :  05 Aug 14  (Deposition) - 01 Oct 14  (Release) - 15 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  H-Nox, Hemoprotein, Gas Sensor, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Herzik, R. Jonnalagadda, J. Kuriyan, M. A. Marletta
Structural Insights Into The Role Of Iron-Histidine Bond Cleavage In Nitric Oxide-Induced Activation Of H-Nox Gas Sensor Proteins.
Proc. Natl. Acad. Sci. Usa V. 111 E4156 2014
PubMed-ID: 25253889  |  Reference-DOI: 10.1073/PNAS.1416936111

(-) Compounds

Molecule 1 - NO-BINDING HEME-DEPENDENT SENSOR PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET20
    Expression System Strain: RP523(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SO_2144
    Mutation: YES
    Organism Scientific: SHEWANELLA ONEIDENSIS
    Organism Taxid: 211586
    Strain: MR-1

 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  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2NA1Ligand/IonSODIUM ION
3ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2NA-1Ligand/IonSODIUM ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2NA-1Ligand/IonSODIUM ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:1 , LYS A:2 , LEU A:77 , HIS A:81 , VAL A:84 , ILE A:102 , HIS A:103 , VAL A:106 , PRO A:113 , SER A:114 , LEU A:115 , PRO A:116 , TYR A:132 , SER A:134 , ARG A:136 , LEU A:145 , LEU A:146 , HOH A:347binding site for residue HEM A 201
2AC2SOFTWARECYS A:139 , HIS A:161 , CYS A:164 , CYS A:172binding site for residue ZN A 202
3AC3SOFTWAREASN A:180 , ASP A:181 , LEU A:184 , HOH A:324 , HOH A:333 , HOH A:354binding site for residue NA A 203
4AC4SOFTWAREMET B:1 , LYS B:2 , LEU B:77 , HIS B:81 , ILE B:98 , ILE B:102 , HIS B:103 , VAL B:106 , PRO B:113 , SER B:114 , LEU B:115 , PRO B:116 , TYR B:132 , SER B:134 , ARG B:136 , LEU B:138 , LEU B:145 , HOH B:327 , HOH B:333binding site for residue HEM B 201
5AC5SOFTWARECYS B:139 , HIS B:161 , CYS B:164 , CYS B:172binding site for residue ZN B 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4U99)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4U99)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4U99)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4U99)

(-) Exons   (0, 0)

(no "Exon" information available for 4U99)

(-) 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:187
                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh...hhhhhhhhhh......eeeeeee...eeeeeee....hhhhhhhhhhhhhhhh..eeeeeeeehhhhh...eeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u99 A   1 MKGIIFNVLEDMVVAQCGMSVWNELLEKHAPKDRVYVSAKSYAESELFSIVQDVAQRLNMPIQDVVKAFGQFLFNGLASRHTDVVDKFDDFTSLVMGIHDVIHLEVNKLYHEPSLPHINGQLLPNNQIALRYSSPRRLCFCAEGLLFGAAQHFAAAIQISHDTCMHTGADHCMLIIELQNDENLYFQ 187
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       


Chain B from PDB  Type:PROTEIN  Length:186
                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh...hhhhhhhhhh......eeeeeee...eeeeeee....hhhhhhhhhhhhhhhh..eeeeeeeehhhhh...eeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4u99 B   1 MKGIIFNVLEDMVVAQCGMSVWNELLEKHAPKDRVYVSAKSYAESELFSIVQDVAQRLNMPIQDVVKAFGQFLFNGLASRHTDVVDKFDDFTSLVMGIHDVIHLEVNKLYHEPSLPHINGQLLPNNQIALRYSSPRRLCFCAEGLLFGAAQHFAAAIQISHDTCMHTGADHCMLIIELQNDENLYF 186
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
   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 4U99)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4U99)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4U99)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)

 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
    HEM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4u99)
 
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
  4u99
    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
  Q8EF49_SHEON | Q8EF49
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q8EF49_SHEON | Q8EF49
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8EF49_SHEON | Q8EF49: 2kii 2kil 4u9b 4u9g 4u9j 4u9k

(-) Related Entries Specified in the PDB File

2kii 2kil 4u9b 4u9g 4u9j 4u9k