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 NFEOB FROM S. THERMOPHILUS BOUND TO GDP.ALF4- AND K+
 
Authors :  M. R. Ash, M. J. Maher, J. M. Guss, M. Jormakka
Date :  08 Jul 11  (Deposition) - 24 Aug 11  (Release) - 27 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.51
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  G Protein, Transmembrane, Iron Transport, Gtpase, Transition-State Analogue, Potassium, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. R. Ash, M. J. Maher, J. M. Guss, M. Jormakka
The Initiation Of Gtp Hydrolysis By The G-Domain Of Feob: Insights From A Transition-State Complex Structure
Plos One V. 6 23355 2011
PubMed-ID: 21858085  |  Reference-DOI: 10.1371/JOURNAL.PONE.0023355

(-) Compounds

Molecule 1 - FERROUS IRON UPTAKE TRANSPORTER PROTEIN B
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-4T-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: NFEOB, UNP RESIDUES 1-270
    Gene: FEOB
    Organism Scientific: STREPTOCOCCUS THERMOPHILUS
    Organism Taxid: 264199
    Strain: LMG 18311
    Synonym: FEOB

 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  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1ALF2Ligand/IonTETRAFLUOROALUMINATE ION
2GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3K2Ligand/IonPOTASSIUM ION
4MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ALF1Ligand/IonTETRAFLUOROALUMINATE ION
2GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3K-1Ligand/IonPOTASSIUM ION
4MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ALF1Ligand/IonTETRAFLUOROALUMINATE ION
2GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3K-1Ligand/IonPOTASSIUM ION
4MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:11 , SER A:12 , GLY A:13 , LYS A:14 , THR A:15 , SER A:16 , VAL A:28 , GLY A:29 , ASN A:30 , ASN A:113 , MET A:114 , ASP A:116 , VAL A:117 , SER A:142 , ALA A:143 , LEU A:144 , HOH A:271 , HOH A:272 , K A:301 , MG A:302 , ALF A:303BINDING SITE FOR RESIDUE GDP A 300
2AC2SOFTWAREASN A:11 , GLY A:29 , TRP A:31 , GDP A:300 , ALF A:303BINDING SITE FOR RESIDUE K A 301
3AC3SOFTWARETHR A:15 , THR A:35 , HOH A:271 , HOH A:272 , GDP A:300 , ALF A:303BINDING SITE FOR RESIDUE MG A 302
4AC4SOFTWAREPRO A:10 , ASN A:11 , LYS A:14 , PRO A:32 , GLY A:33 , VAL A:34 , THR A:35 , GLY A:56 , HOH A:271 , HOH A:272 , HOH A:273 , GDP A:300 , K A:301 , MG A:302BINDING SITE FOR RESIDUE ALF A 303
5AC5SOFTWAREASN B:11 , SER B:12 , GLY B:13 , LYS B:14 , THR B:15 , SER B:16 , GLY B:29 , ASN B:30 , ASN B:113 , MET B:114 , ASP B:116 , VAL B:117 , SER B:142 , ALA B:143 , LEU B:144 , HOH B:272 , K B:301 , MG B:302 , ALF B:303BINDING SITE FOR RESIDUE GDP B 300
6AC6SOFTWAREASN B:11 , GLY B:29 , TRP B:31 , GDP B:300 , ALF B:303BINDING SITE FOR RESIDUE K B 301
7AC7SOFTWARETHR B:15 , THR B:35 , HOH B:271 , HOH B:272 , GDP B:300 , ALF B:303BINDING SITE FOR RESIDUE MG B 302
8AC8SOFTWAREPRO B:10 , ASN B:11 , LYS B:14 , PRO B:32 , GLY B:33 , VAL B:34 , THR B:35 , GLY B:56 , HOH B:271 , HOH B:272 , HOH B:273 , GDP B:300 , K B:301 , MG B:302BINDING SITE FOR RESIDUE ALF B 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3SS8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3SS8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SS8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3SS8)

(-) Exons   (0, 0)

(no "Exon" information available for 3SS8)

(-) 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:257
 aligned with Q5M586_STRT2 | Q5M586 from UniProtKB/TrEMBL  Length:712

    Alignment length:257
                                    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       
         Q5M586_STRT2     1 MTEIALIGNPNSGKTSLFNLITGHNQRVGNWPGVTVERKSGLVKKNKDLEIQDLPGIYSMSPYSPEEKVARDYLLSQRADSILNVVDATNLERNLYLTTQLIETGIPVTIALNMIDVLDGQGKKINVDKLSYHLGVPVVATSALKQTGVDQVVKKAAHTTTSTVGDLAFPIYDDRLEAAISQILEVLGNSVPQRSARFYAIKLFEQDSLVEAELDLSQFQRKEIEDIIRITEEIFTEDAESIVINERYAFIERVCQM 257
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhh...............eeeee..eeeeeeee..........hhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhh...eeeeeehhhhhhhh....hhhhhhhhhh..eee.......hhhhhhhhhhh..............hhhhhhhhhhhhhhhh......hhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ss8 A   1 MTEIALIGNPNSGKTSLFNLITGHNQRVGNWPGVTVERKSGLVKKNKDLEIQDLPGIYSMSPYSPEEKVARDYLLSQRADSILNVVDATNLERNLYLTTQLIETGIPVTIALNMIDVLDGQGKKINVDKLSYHLGVPVVATSALKQTGVDQVVKKAAHTTTSTVGDLAFPIYDDRLEAAISQILEVLGNSVPQRSARFYAIKLFEQDSLVEAELDLSQFQRKEIEDIIRITEEIFTEDAESIVINERYAFIERVCQM 257
                                    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       


Chain B from PDB  Type:PROTEIN  Length:257
 aligned with Q5M586_STRT2 | Q5M586 from UniProtKB/TrEMBL  Length:712

    Alignment length:257
                                    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       
         Q5M586_STRT2     1 MTEIALIGNPNSGKTSLFNLITGHNQRVGNWPGVTVERKSGLVKKNKDLEIQDLPGIYSMSPYSPEEKVARDYLLSQRADSILNVVDATNLERNLYLTTQLIETGIPVTIALNMIDVLDGQGKKINVDKLSYHLGVPVVATSALKQTGVDQVVKKAAHTTTSTVGDLAFPIYDDRLEAAISQILEVLGNSVPQRSARFYAIKLFEQDSLVEAELDLSQFQRKEIEDIIRITEEIFTEDAESIVINERYAFIERVCQM 257
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....hhhhhhhhhhh...............eeeee..eeeeeeee..........hhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhh....eeeeeehhhhhhhh....hhhhhhhhhh..eee.......hhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ss8 B   1 MTEIALIGNPNSGKTSLFNLITGHNQRVGNWPGVTVERKSGLVKKNKDLEIQDLPGIYSMSPYSPEEKVARDYLLSQRADSILNVVDATNLERNLYLTTQLIETGIPVTIALNMIDVLDGQGKKINVDKLSYHLGVPVVATSALKQTGVDQVVKKAAHTTTSTVGDLAFPIYDDRLEAAISQILEVLGNSVPQRSARFYAIKLFEQDSLVEAELDLSQFQRKEIEDIIRITEEIFTEDAESIVINERYAFIERVCQM 257
                                    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
   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 3SS8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3SS8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SS8)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q5M586_STRT2 | Q5M586)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0015093    ferrous iron transmembrane transporter activity    Enables the transfer of ferrous iron (Fe(II) or Fe2+) ions from one side of a membrane to the other.
biological process
    GO:1903874    ferrous iron transmembrane transport    The directed movement of ferrous iron (iron(2+)) across a membrane.
    GO:0015684    ferrous iron transport    The directed movement of ferrous iron (Fe(II) or Fe2+) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0055072    iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions within an organism or cell.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

 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
    ALF  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GDP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    K  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ 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 ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3ss8)
 
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
  3ss8
    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
  Q5M586_STRT2 | Q5M586
    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
  Q5M586_STRT2 | Q5M586
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q5M586_STRT2 | Q5M586: 3b1v 3b1w 3b1x 3b1y 3b1z 3lx5 3lx8 3tah 4non

(-) Related Entries Specified in the PDB File

3lx5 CRYSTAL STRUCTURE OF MGMPPNP-BOUND NFEOB FROM S. THERMOPHILUS
3lx8 CRYSTAL STRUCTURE OF GDP-BOUND NFEOB FROM S. THERMOPHILUS