Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE HETERODIMERIC CATALYTIC DOMAIN OF WILD-TYPE HUMAN SOLUBLE GUANYLATE CYCLASE
 
Authors :  F. Seeger, G. J. Williams, J. A. Tainer, E. D. Garcin
Date :  05 Nov 13  (Deposition) - 16 Apr 14  (Release) - 07 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Heterodimeric, Lyase, Cgmp Biosynthesis, Nitric Oxide, Cyclase, Gtp- Binding, Metal-Binding, Nucleotide Binding, Cytosol (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Seeger, R. Quintyn, A. Tanimoto, G. J. Williams, J. A. Tainer, V. H. Wysocki, E. D. Garcin
Interfacial Residues Promote An Optimal Alignment Of The Catalytic Center In Human Soluble Guanylate Cyclase: Heterodimerization Is Required But Not Sufficient For Activity.
Biochemistry V. 53 2153 2014
PubMed-ID: 24669844  |  Reference-DOI: 10.1021/BI500129K

(-) Compounds

Molecule 1 - GUANYLATE CYCLASE SOLUBLE SUBUNIT ALPHA-3
    Chains: A
    EC Number: 4.6.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNH-TRXT
    Expression System Strain: BL21(DE3) PGRO7 CHAPERONE
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN, UNP RESIDUES 468-661
    Gene: GUC1A3, GUCSA3, GUCY1A1, GUCY1A3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GCS-ALPHA-3, GCS-ALPHA-1, SOLUBLE GUANYLATE CYCLASE LARGE SUBUNIT
 
Molecule 2 - GUANYLATE CYCLASE SOLUBLE SUBUNIT BETA-1
    Chains: B
    EC Number: 4.6.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC-CTHF
    Expression System Strain: BL21(DE3) PGRO7 CHAPERONE
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN, UNP RESIDUES 408-608
    Gene: GUC1B3, GUCSB3, GUCY1B1, GUCY1B3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GCS-BETA-1, GUANYLATE CYCLASE SOLUBLE SUBUNIT BETA-3, GCS- BETA-3, SOLUBLE GUANYLATE CYCLASE SMALL SUBUNIT

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:525 , GLU A:526 , LEU A:596 , HOH A:810 , HOH A:839BINDING SITE FOR RESIDUE EDO A 701
2AC2SOFTWAREASP A:486 , ILE A:487 , TYR A:510 , GLY A:529 , ALA A:531 , HOH A:812 , HOH A:868BINDING SITE FOR RESIDUE EDO A 702
3AC3SOFTWAREILE A:528 , GLY A:529 , HOH A:877 , GLU B:473 , THR B:474 , MET B:480 , HOH B:837BINDING SITE FOR RESIDUE EDO B 701
4AC4SOFTWARELYS A:590 , PHE B:468 , GLY B:484 , LEU B:485 , PRO B:486 , GLU B:487BINDING SITE FOR RESIDUE EDO B 702
5AC5SOFTWAREILE B:427 , VAL B:428 , THR B:520 , GLU B:554 , HOH B:828 , HOH B:896BINDING SITE FOR RESIDUE EDO B 703
6AC6SOFTWAREVAL B:428 , GLY B:429 , HOH B:812BINDING SITE FOR RESIDUE EDO B 704

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NI2)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu B:485 -Pro B:486

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NI2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NI2)

(-) Exons   (0, 0)

(no "Exon" information available for 4NI2)

(-) Sequences/Alignments

Asymmetric/Biological 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:192
                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.......eeee.......hhhhhhhhhhhhhhhhhh...........eeeeeeeeeeeeeee.....eeeeehhhhhhhhhhhhh.....eeehhhhhhhhh....eeeee..................eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ni2 A 471 VVQAKKFSNVTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHKESDTHAVQIALMALKMMELSDEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPGFVFTPRSREELPPNFPSEIPGICHFLDAYQQ 662
                                   480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660  


Chain B from PDB  Type:PROTEIN  Length:198
                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeeeeeeee.hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.......eee......eeeee.......hhhhhhhhhhhhhhhhhh..ee..ee..eeeeeeeeeeeeeee.....eeeeehhhhhhhhhhhhh.....eeeehhhhhhhh........eeeeeeeee........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ni2 B 411 PVPAKRYDNVTILFSGIVGFNAFCSKHASGEGAMKIVNLLNDLYTRFDTLTDSRKNPFVYKVETVGDKYMTVSGLPEPCIHHARSICHLALDMMEIAGQVQVDGESVQITIGIHTGEVVTGVIGQRMPRYCLFGNTVNLTSRTETTGEKGKINVSEYTYRCLMSPENSDPQFHLEHRGPVSMKGKKEPMQVWFLSRKN 608
                                   420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600
   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 4NI2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NI2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NI2)

(-) Gene Ontology  (30, 47)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    EDO  [ 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 ]
 
  Cis Peptide Bonds
    Leu B:485 - Pro B:486   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  4ni2
    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
  GCYA3_HUMAN | Q02108
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  GCYB1_HUMAN | Q02153
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  4.6.1.2
    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
  GCYA3_HUMAN | Q02108
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  GCYB1_HUMAN | Q02153
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        GCYA3_HUMAN | Q02108: 3uvj
        GCYB1_HUMAN | Q02153: 2wz1 3uvj

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4NI2)