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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF STACHYDRINE DEMETHYLASE IN COMPLEX WITH CYANIDE, OXYGEN, AND N-METHYL PROLINE IN A NEW ORIENTATION
 
Authors :  R. Agarwal, B. Andi, A. Gizzi, J. B. Bonanno, S. C. Almo, A. M. Orville
Date :  11 Jul 14  (Deposition) - 15 Jul 15  (Release) - 09 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.76
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Composite Datasets, Photoelectron, Enzyme-Catalyzed Reactions, Cyanide, Synchrotron, Rieske Type Monoxygenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Agarwal, B. Andi, A. Gizzi, J. B. Bonanno, S. C. Almo, A. M. Orville
Tracking Photoelectron Induced In-Crystallo Enzyme Catalysi
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MONOXYGENASE; DEMETHYLASE
    Chains: A
    EC Number: 1.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PSGC
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SMA0751
    Organism Common: ENSIFER MELILOTI
    Organism Scientific: SINORHIZOBIUM MELILOTI 1021
    Organism Taxid: 266834
    Synonym: STACHYDRINE DEMETHYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 7)

Asymmetric Unit (7, 7)
No.NameCountTypeFull Name
13BY1Ligand/Ion1-METHYL-L-PROLINE
2CYN1Ligand/IonCYANIDE ION
3FE1Ligand/IonFE (III) ION
4FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
5NCO1Ligand/IonCOBALT HEXAMMINE(III)
6OXY1Ligand/IonOXYGEN MOLECULE
7TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (6, 18)
No.NameCountTypeFull Name
13BY3Ligand/Ion1-METHYL-L-PROLINE
2CYN3Ligand/IonCYANIDE ION
3FE-1Ligand/IonFE (III) ION
4FES3Ligand/IonFE2/S2 (INORGANIC) CLUSTER
5NCO3Ligand/IonCOBALT HEXAMMINE(III)
6OXY3Ligand/IonOXYGEN MOLECULE
7TRS3Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:86 , HIS A:88 , ARG A:89 , CYS A:106 , HIS A:109 , TRP A:111BINDING SITE FOR RESIDUE FES A 501
2AC2SOFTWAREHIS A:204 , HIS A:209 , ASP A:360 , OXY A:506 , CYN A:507BINDING SITE FOR RESIDUE FE A 502
3AC3SOFTWAREARG A:14 , ARG A:15 , LEU A:16 , GLU A:22 , PRO A:378 , HOH A:784 , HOH A:819 , HOH A:827BINDING SITE FOR RESIDUE TRS A 503
4AC4SOFTWARELEU A:12 , ASP A:13 , ARG A:15 , HOH A:817BINDING SITE FOR RESIDUE NCO A 504
5AC5SOFTWAREASN A:199 , GLU A:201 , CYS A:202 , PHE A:216 , ALA A:223 , TRP A:305 , HIS A:307 , TRP A:353 , OXY A:506 , CYN A:507 , HOH A:646 , HOH A:854BINDING SITE FOR RESIDUE 3BY A 505
6AC6SOFTWAREASN A:198 , HIS A:204 , HIS A:209 , ASP A:360 , FE A:502 , 3BY A:505BINDING SITE FOR RESIDUE OXY A 506
7AC7SOFTWAREHIS A:204 , HIS A:209 , ASP A:360 , FE A:502 , 3BY A:505BINDING SITE FOR RESIDUE CYN A 507

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:202 -A:205

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:289 -Pro A:290
2Tyr A:301 -Pro A:302

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QUR)

(-) 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:415
                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...hhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeeee.hhhh...eeeeeee..eeeeeee.....eeeee..............eee...ee......ee.....eee........hhhhh...eeeeeee..eeeee.......hhhhhhhhhhhhhhhhhh.eeeeeeeeeee..hhhhhhhhhh...hhhhhh.hhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhh......ee.....eeeeee..............................eeeeee...eeeee....eeeeeeeeee..eeeeeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qur A  -9 GTENLYFQSMMTANPTSIHQRLDRRLSGFSLEQPFYTSPEVYALDLQHIFYKQWLYAVPVCQLAKAGSYTTLRVGAYEVVIVRSRDGEVRAFHNSCRHRGSLICKARQGQVAKLVCPYHQWTYELDGKLIWANDMGPDFDASKYGLKPVNLRNLDGLIYICLSDTPPDFQTFAQLARPYLEVHDLKDAKVAFTSTIIEKGNWKLVWENNRECYHCSSNHPALCRSFPLDPEVAGVQADGGVSKKLQAHFDRCEAAGTPAQFVLAGDGQYRLARMPLQEKALSYTMDGKAAVSRHLGRVAPPDAGTLLMFHYPSTWNHFLPDHSLTFRVMPISPTETEVTTTWLVHKDAVEGVDYDLKRLTEVWIATNDEDREIVETNQQGILSPAYVPGPYSPGQESGVMQFVDWYAASLERALA 405
                                     0        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       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400
   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 4QUR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

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
    3BY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CYN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FES  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NCO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OXY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TRS  [ 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 ]
 
  Cis Peptide Bonds
    Ala A:289 - Pro A:290   [ RasMol ]  
    Tyr A:301 - Pro A:302   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  4qur
    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
  Q92ZP9_RHIME | Q92ZP9
    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)
  1.-.-.-
    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
  Q92ZP9_RHIME | Q92ZP9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q92ZP9_RHIME | Q92ZP9: 3vca 3vcp 4qup 4quq 5hl4

(-) Related Entries Specified in the PDB File

3vca 3vcp 4qup 4quq