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 OXYGEN BINDING H-NOX DOMAIN RELATED TO SOLUBLE GUANYLATE CYCLASES (OXYGEN COMPLEX)
 
Authors :  P. Pellicena, D. S. Karow, E. M. Boon, M. A. Marletta, J. Kuriyan
Date :  25 Jul 04  (Deposition) - 31 Aug 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.07
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  H-Nox Domain, Heme, Oxygen Sensor, Signal Transduction, Chemotaxis, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Pellicena, D. S. Karow, E. M. Boon, M. A. Marletta, J. Kuriyan
Crystal Structure Of An Oxygen-Binding Heme Domain Related To Soluble Guanylate Cyclases.
Proc. Natl. Acad. Sci. Usa V. 101 12854 2004
PubMed-ID: 15326296  |  Reference-DOI: 10.1073/PNAS.0405188101

(-) Compounds

Molecule 1 - HEME-BASED METHYL-ACCEPTING CHEMOTAXIS PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-20B
    Expression System Strain: TUNER DE3 PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: H-NOX DOMAIN
    Gene: TAR4
    Organism Scientific: THERMOANAEROBACTER TENGCONGENSIS
    Organism Taxid: 119072

 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  (5, 23)

Asymmetric Unit (5, 23)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3MSE14Mod. Amino AcidSELENOMETHIONINE
4OXY2Ligand/IonOXYGEN MOLECULE
5SCN1Ligand/IonTHIOCYANATE ION
Biological Unit 1 (4, 12)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3MSE7Mod. Amino AcidSELENOMETHIONINE
4OXY1Ligand/IonOXYGEN MOLECULE
5SCN-1Ligand/IonTHIOCYANATE ION
Biological Unit 2 (5, 11)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3MSE7Mod. Amino AcidSELENOMETHIONINE
4OXY1Ligand/IonOXYGEN MOLECULE
5SCN1Ligand/IonTHIOCYANATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:38 , PRO A:39 , LEU A:40 , LYS B:2 , THR B:4 , PHE B:82BINDING SITE FOR RESIDUE SCN B 197
2AC2SOFTWARELYS A:2 , ILE A:5 , PHE A:78 , MSE A:98 , HIS A:102 , LEU A:105 , THR A:113 , PRO A:114 , PRO A:115 , MSE A:129 , TYR A:131 , SER A:133 , ARG A:135 , MSE A:137 , TYR A:140 , PHE A:141 , LEU A:144 , GOL A:193 , OXY A:501BINDING SITE FOR RESIDUE HEM A 500
3AC3SOFTWAREPHE A:78 , TYR A:140 , LEU A:144 , HEM A:500BINDING SITE FOR RESIDUE OXY A 501
4AC4SOFTWAREMSE B:1 , LYS B:2 , ILE B:5 , PHE B:78 , MSE B:98 , HIS B:102 , LEU B:105 , THR B:113 , PRO B:114 , PRO B:115 , LEU B:117 , MSE B:129 , TYR B:131 , SER B:133 , ARG B:135 , TYR B:140 , LEU B:144 , OXY B:503 , HOH B:514 , HOH B:526BINDING SITE FOR RESIDUE HEM B 502
5AC5SOFTWAREPHE B:78 , TYR B:140 , HEM B:502BINDING SITE FOR RESIDUE OXY B 503
6AC6SOFTWAREMSE A:1 , LYS A:2 , ASP A:42 , ILE A:109 , ALA A:112 , THR A:113 , ARG A:135 , HEM A:500BINDING SITE FOR RESIDUE GOL A 193
7AC7SOFTWARELEU A:40 , HOH A:586 , THR B:4 , ILE B:37 , PRO B:39BINDING SITE FOR RESIDUE GOL A 194
8AC8SOFTWAREARG A:49 , ASN A:64 , TRP A:67 , ARG A:135 , LYS A:136 , HOH A:573BINDING SITE FOR RESIDUE GOL A 195
9AC9SOFTWAREVAL B:48 , ARG B:49 , ARG B:135BINDING SITE FOR RESIDUE GOL B 196

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U4H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1U4H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U4H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1U4H)

(-) Exons   (0, 0)

(no "Exon" information available for 1U4H)

(-) 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:188
 aligned with Q8RBX6_CALS4 | Q8RBX6 from UniProtKB/TrEMBL  Length:602

    Alignment length:188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        
         Q8RBX6_CALS4     1 MKGTIVGTWIKTLRDLYGNDVVDESLKSVGWEPDRVITPLEDIDDDEVRRIFAKVSEKTGKNVNEIWREVGRQNIKTFSEWFPSYFAGRRLVNFLMMMDEVHLQLTKMIKGATPPRLIAKPVAKDAIEMEYVSKRKMYDYFLGLIEGSSKFFKEEISVEEVERGEKDGFSRLKVRIKFKNPVFEYKKN 188
               SCOP domains d1u4ha_ A: Methyl-accepting chemotaxis protein                                                                                                                                               SCOP domains
               CATH domains -1u4hA00 A:2-188 H-NOX domain                                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.............eeeee..eeeeeeee...hhhhhhhhhhhhhhhh...eeeeeeeeeee..eeeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u4h A   1 mKGTIVGTWIKTLRDLYGNDVVDESLKSVGWEPDRVITPLEDIDDDEVRRIFAKVSEKTGKNVNEIWREVGRQNIKTFSEWFPSYFAGRRLVNFLmmmDEVHLQLTKmIKGATPPRLIAKPVAKDAIEmEYVSKRKmYDYFLGLIEGSSKFFKEEISVEEVERGEKDGFSRLKVRIKFKNPVFEYKKN 188
                            |       10        20        30        40        50        60        70        80        90     ||100       110       120       130      |140       150       160       170       180        
                            |                                                                                             96-MSE     108-MSE              129-MSE 137-MSE                                               
                            1-MSE                                                                                          97-MSE                                                                                       
                                                                                                                            98-MSE                                                                                      


Chain B from PDB  Type:PROTEIN  Length:188
 aligned with Q8RBX6_CALS4 | Q8RBX6 from UniProtKB/TrEMBL  Length:602

    Alignment length:188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        
         Q8RBX6_CALS4     1 MKGTIVGTWIKTLRDLYGNDVVDESLKSVGWEPDRVITPLEDIDDDEVRRIFAKVSEKTGKNVNEIWREVGRQNIKTFSEWFPSYFAGRRLVNFLMMMDEVHLQLTKMIKGATPPRLIAKPVAKDAIEMEYVSKRKMYDYFLGLIEGSSKFFKEEISVEEVERGEKDGFSRLKVRIKFKNPVFEYKKN 188
               SCOP domains d1u4hb_ B: Methyl-accepting chemotaxis protein                                                                                                                                               SCOP domains
               CATH domains -1u4hB00 B:2-188 H-NOX domain                                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh........eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhhh..eeeeeeeeeee..eeeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u4h B   1 mKGTIVGTWIKTLRDLYGNDVVDESLKSVGWEPDRVITPLEDIDDDEVRRIFAKVSEKTGKNVNEIWREVGRQNIKTFSEWFPSYFAGRRLVNFLmmmDEVHLQLTKmIKGATPPRLIAKPVAKDAIEmEYVSKRKmYDYFLGLIEGSSKFFKEEISVEEVERGEKDGFSRLKVRIKFKNPVFEYKKN 188
                            |       10        20        30        40        50        60        70        80        90     ||100       110       120       130      |140       150       160       170       180        
                            1-MSE                                                                                         96-MSE     108-MSE              129-MSE 137-MSE                                               
                                                                                                                           97-MSE                                                                                       
                                                                                                                            98-MSE
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1U4H)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8RBX6_CALS4 | Q8RBX6)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
biological process
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
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.

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HEM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OXY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SCN  [ 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 ]
    AC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1u4h)
 
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
  1u4h
    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
  Q8RBX6_CALS4 | Q8RBX6
    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
  Q8RBX6_CALS4 | Q8RBX6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8RBX6_CALS4 | Q8RBX6: 1u55 1u56 1xbn 3eee 3iqb 3lah 3lai 3m0b 3nvr 3nvu 3sj5 3tf0 3tf1 4fdk 4it2 5jru 5jrv 5jrx

(-) Related Entries Specified in the PDB File

1u55 1u56