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 PLP-DEPENDENT CYCLASE ORFR IN COMPLEX WITH PLP-L-ARG
 
Authors :  C. Y. Chang, Y. C. Liu, S. Y. Lyu, C. C. Wu, T. L. Li
Date :  05 Aug 13  (Deposition) - 18 Jun 14  (Release) - 18 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.58
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Cyclase, Plp Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Y. Chang, S. Y. Lyu, Y. C. Liu, N. S. Hsu, C. C. Wu, C. F. Tang, K. H. Lin, J. Y. Ho, C. J. Wu, M. D. Tsai, T. L. Li
Biosynthesis Of Streptolidine Involved Two Unexpected Intermediates Produced By A Dihydroxylase And A Cyclase Through Unusual Mechanisms.
Angew. Chem. Int. Ed. Engl. V. 53 1943 2014
PubMed-ID: 24505011  |  Reference-DOI: 10.1002/ANIE.201307989

(-) Compounds

Molecule 1 - AMINOTRANSFERASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: STREPTOMYCES LAVENDULAE
    Organism Taxid: 58340

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1ARG1Mod. Amino AcidARGININE
2PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1ARG2Mod. Amino AcidARGININE
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:90 , SER A:91 , SER A:92 , TYR A:116 , ASN A:162 , ASN A:166 , ASP A:194 , THR A:222 , SER A:224 , LYS A:225 , ARG A:233 , ARG A:402 , HOH A:577 , HOH A:594BINDING SITE FOR RESIDUE PLP A 401
2AC2SOFTWARELEU A:14 , GLU A:15 , TYR A:18 , SER A:32 , ASP A:60 , TYR A:116 , ASN A:166 , LYS A:225 , PHE A:257 , ARG A:358 , PLP A:401 , HOH A:501 , HOH A:563 , HOH A:583BINDING SITE FOR RESIDUE ARG A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4M2M)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:163 -Pro A:164
2Asn A:166 -Pro A:167

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M2M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M2M)

(-) Exons   (0, 0)

(no "Exon" information available for 4M2M)

(-) 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:381
                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhh....ee.........hhhhhhhhh..hhhhhhh..........hhhhhhhhhhhhh..hhh.eeeehhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhh..eeeeehhh.ee..eehhhhhhhhh.....eeeee..........hhhhhhhhhhhhhhhh.eeeee..............hhhhhh...eeeee......hhhhh.eeee.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee........ee..eehhhhhh....hhhhhhhhhhhhhhhee.ee.hhhh....eeee...hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m2m A   6 PRREDPPVLEEWYRRHLGPDIHDISSSGVHPYSFAEIRDVCRIPAADLDAVVMDDSVSQGGEGVRRAIADRYAGGDADRVLVTHGSSEAIALTLNALLHRGDRVVVQEGIYHSLGHYPRAAGCDVAVLPGRAVRDGEIDPDVLAGLVTPGTAAVIVNFPHNPTGVTLSPQGLRALKERTAATGAVLVWDAATAEIAHRWEVLADPGADGGDTVSYGTLSKTFGLPGLRVGWAVAPKELLTATFPLRDRTTLFLSPLVELVAERAVRHADELIGARAAEARHNLAHLTGWMAAHEELVRWTPPEGGVCALPVFRELERAAAGPQEVERFCLELLERHRTLLVPGTAFGAPHGARLGFGGPQEDFRAGLDGLSRFLRERAAGR 402
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385|
                                                                                                                                                                                                                                                                                                                                                                                                                     385|
                                                                                                                                                                                                                                                                                                                                                                                                                      402
   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 4M2M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M2M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M2M)

(-) 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
    ARG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PLP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asn A:166 - Pro A:167   [ RasMol ]  
    Phe A:163 - Pro A:164   [ 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
  4m2m
    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
  G9MBV4_STRLA | G9MBV4
    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
  G9MBV4_STRLA | G9MBV4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        G9MBV4_STRLA | G9MBV4: 4m2j 4m2k

(-) Related Entries Specified in the PDB File

4m23 4m25 4m26 4m27 4m2c 4m2e 4m2f 4m2g 4m2i 4m2j 4m2k