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 :  PSEUDOMONAS AERUGINOSA RMLA IN COMPLEX WITH ALLOSTERIC INHIBITOR
 
Authors :  M. S. Alphey, F. Tran, N. J. Westwood, J. H. Naismith
Date :  19 Jan 16  (Deposition) - 22 Feb 17  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  C,D  (2x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Thymidylyl, Transferase, Allosteric, Inhibitor, Pseudomonas (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Tran, M. S. Alphey, N. J. Westwood, J. H. Naismith
Allosteric Competitive Inhibitors Of The Glucose-1-Phosphat Thymidylyltransferase (Rmla) From Pseudomonas Aeruginosa.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
    Chains: A, B, C, D
    EC Number: 2.7.7.24
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x):   CD
Biological Unit 2 (2x): AB  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2FKH4Ligand/IonN-(6-AMINO-1-(3-METHYLBENZYL)-2,4-DIOXO-1,2,3,4-TETRAHYDROPYRIMIDIN-5-YL)-N-METHYLBENZENESULFONAMIDE
3MES4Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FKH4Ligand/IonN-(6-AMINO-1-(3-METHYLBENZYL)-2,4-DIOXO-1,2,3,4-TETRAHYDROPYRIMIDIN-5-YL)-N-METHYLBENZENESULFONAMIDE
3MES4Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FKH4Ligand/IonN-(6-AMINO-1-(3-METHYLBENZYL)-2,4-DIOXO-1,2,3,4-TETRAHYDROPYRIMIDIN-5-YL)-N-METHYLBENZENESULFONAMIDE
3MES4Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:41 , LEU A:45 , TYR A:113 , TYR A:114 , GLY A:115 , PHE A:118 , ARG A:219 , VAL A:250 , ALA A:251 , GLU A:255 , ILE A:256 , HOH A:2125 , HOH A:2130 , HOH A:2223 , HOH A:2256BINDING SITE FOR RESIDUE FKH A 1294
02AC2SOFTWAREGLY A:154 , LYS A:155 , ALA A:156 , SER A:213 , VAL A:214 , ILE A:216BINDING SITE FOR RESIDUE MES A 1295
03AC3SOFTWARESER B:41 , LEU B:45 , TYR B:113 , TYR B:114 , GLY B:115 , PHE B:118 , HIS B:119 , ARG B:219 , LYS B:249 , VAL B:250 , ALA B:251 , GLU B:255 , ILE B:256 , ARG B:259 , HOH B:2117 , HOH B:2229BINDING SITE FOR RESIDUE FKH B 1294
04AC4SOFTWAREGLY B:154 , LYS B:155 , ALA B:156 , VAL B:214 , ILE B:216 , HOH B:2156 , HOH B:2211 , HOH B:2264BINDING SITE FOR RESIDUE MES B 1295
05AC5SOFTWARESER C:41 , LEU C:45 , TYR C:113 , TYR C:114 , GLY C:115 , PHE C:118 , HIS C:119 , ARG C:219 , VAL C:250 , ALA C:251 , GLU C:255 , ILE C:256 , ARG C:259 , HOH C:2105 , HOH C:2110 , HOH C:2203 , HOH C:2246BINDING SITE FOR RESIDUE FKH C 1294
06AC6SOFTWAREPHE C:150 , GLY C:154 , ALA C:156 , SER C:213 , VAL C:214 , ILE C:216 , HOH C:2178 , HOH C:2247 , HOH C:2248BINDING SITE FOR RESIDUE MES C 1295
07AC7SOFTWARESER D:41 , LEU D:45 , TYR D:113 , TYR D:114 , GLY D:115 , HIS D:119 , ARG D:219 , VAL D:250 , ALA D:251 , GLU D:255 , ILE D:256 , ARG D:259 , HOH D:2088 , HOH D:2090 , HOH D:2167 , HOH D:2204BINDING SITE FOR RESIDUE FKH D 1294
08AC8SOFTWAREGLY D:154 , ALA D:156 , SER D:213 , VAL D:214 , ILE D:216 , HOH D:2116 , HOH D:2205BINDING SITE FOR RESIDUE MES D 1295
09AC9SOFTWAREHIS A:116 , GLY A:218 , ARG A:219 , GLY A:220BINDING SITE FOR RESIDUE CL A 1296
10BC1SOFTWAREHIS B:116 , GLY B:218 , ARG B:219 , GLY B:220BINDING SITE FOR RESIDUE CL B 1296
11BC2SOFTWAREHIS C:116 , GLY C:218 , ARG C:219 , GLY C:220BINDING SITE FOR RESIDUE CL C 1296
12BC3SOFTWAREHIS D:116 , GLY D:218 , ARG D:219 , GLY D:220BINDING SITE FOR RESIDUE CL D 1296

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FU0)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1His A:17 -Pro A:18
2His B:17 -Pro B:18
3His C:17 -Pro C:18
4His D:17 -Pro D:18

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FU0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FU0)

(-) Exons   (0, 0)

(no "Exon" information available for 5FU0)

(-) 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:296
                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee..............hhhh.ee..ee.hhhhhhhhhhh...eeeeee...hhhhhhhhhh.hhhhh.eeeeee.....hhhhhhhhhhhhhh..eeeeee...eee..hhhhhhhhhhhh...eeeeeee..hhhh.eeeee.....eeeeee........eee..eeee..hhhhhhhh.........hhhhhhhhhhhh..eeeee.....eee...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fu0 A  -9 HHHHKRKGIILAGGSGTRLHPATLAISKQLLPVYDKPMIYYPLSTLMLAGIREILIISTPQDTPRFQQLLGDGSNWGLDLQYAVQPSPDGLAQAFLIGESFIGNDLSALVLGDNLYYGHDFHELLGSASQRQTGASVFAYHVLDPERYGVVEFDQGGKAISLEEKPLEPKSNYAVTGLYFYDQQVVDIARDLKPSPRGELEITDVNRAYLERGQLSVEIMGRGYAWLDTGTHDSLLEAGQFIATLENRQGLKVACPEEIAYRQKWIDAAQLEKLAAPLAKNGYGQYLKRLLTETVY 293
                               ||    7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287      
                              -6|                                                                                                                                                                                                                                                                                                   
                                2                                                                                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:293
                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..............hhhh.ee..ee.hhhhhhhhhhh...eeeeee...hhhhhhhhhh.hhhhh.eeeeee.......hhhhhhhhhhhh..eeeeee...eee..hhhhhhhhhhhh...eeeeeee..hhhh.eeeee.....eeeeee........eee..eeee..hhhhhhhh.........hhhhhhhhhhhh..eeeee.....eee...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhh...hhhhhhhhhh....hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fu0 B   1 MKRKGIILAGGSGTRLHPATLAISKQLLPVYDKPMIYYPLSTLMLAGIREILIISTPQDTPRFQQLLGDGSNWGLDLQYAVQPSPDGLAQAFLIGESFIGNDLSALVLGDNLYYGHDFHELLGSASQRQTGASVFAYHVLDPERYGVVEFDQGGKAISLEEKPLEPKSNYAVTGLYFYDQQVVDIARDLKPSPRGELEITDVNRAYLERGQLSVEIMGRGYAWLDTGTHDSLLEAGQFIATLENRQGLKVACPEEIAYRQKWIDAAQLEKLAAPLAKNGYGQYLKRLLTETVY 293
                                    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   


Chain C from PDB  Type:PROTEIN  Length:296
                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee.........hhhhhhhhhh.ee..ee.hhhhhhhhhhh...eeeeee...hhhhhhhhhh.hhhhh.eeeeee.....hhhhhhhhhhhhhh..eeeeee..eeee..hhhhhhhhhhhh...eeeeeee..hhhh.eeeee.....eeeeee........eee..eeee..hhhhhhhh.........hhhhhhhhhhhh..eeeee.....eeee..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fu0 C  -9 HHHHKRKGIILAGGSGTRLHPATLAISKQLLPVYDKPMIYYPLSTLMLAGIREILIISTPQDTPRFQQLLGDGSNWGLDLQYAVQPSPDGLAQAFLIGESFIGNDLSALVLGDNLYYGHDFHELLGSASQRQTGASVFAYHVLDPERYGVVEFDQGGKAISLEEKPLEPKSNYAVTGLYFYDQQVVDIARDLKPSPRGELEITDVNRAYLERGQLSVEIMGRGYAWLDTGTHDSLLEAGQFIATLENRQGLKVACPEEIAYRQKWIDAAQLEKLAAPLAKNGYGQYLKRLLTETVY 293
                               ||    7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287      
                              -6|                                                                                                                                                                                                                                                                                                   
                                2                                                                                                                                                                                                                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:292
                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.........hhhhhhhhhh.ee..ee.hhhhhhhhhhh...eeeeee...hhhhhhhhhh.hhhhh.eeeeee.....hhhhhhhhhhhhhh..eeeeee..eeee..hhhhhhhhhhhh...eeeeeee..hhhh.eeeee.....eeeeee........eee..eeee..hhhhhhhh.........hhhhhhhhhhhh..eeeee.....eeee..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fu0 D   2 KRKGIILAGGSGTRLHPATLAISKQLLPVYDKPMIYYPLSTLMLAGIREILIISTPQDTPRFQQLLGDGSNWGLDLQYAVQPSPDGLAQAFLIGESFIGNDLSALVLGDNLYYGHDFHELLGSASQRQTGASVFAYHVLDPERYGVVEFDQGGKAISLEEKPLEPKSNYAVTGLYFYDQQVVDIARDLKPSPRGELEITDVNRAYLERGQLSVEIMGRGYAWLDTGTHDSLLEAGQFIATLENRQGLKVACPEEIAYRQKWIDAAQLEKLAAPLAKNGYGQYLKRLLTETVY 293
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291
   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 5FU0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FU0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FU0)

(-) Gene Ontology  (7, 7)

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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FKH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MES  [ 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 ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    His A:17 - Pro A:18   [ RasMol ]  
    His B:17 - Pro B:18   [ RasMol ]  
    His C:17 - Pro C:18   [ RasMol ]  
    His D:17 - Pro D:18   [ RasMol ]  
 
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
  5fu0
    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
  Q9HU22_PSEAE | Q9HU22
    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)
  2.7.7.24
    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
  Q9HU22_PSEAE | Q9HU22
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9HU22_PSEAE | Q9HU22: 1fxo 1fzw 1g0r 1g1l 1g23 1g2v 1g3l 3zlk 3zll 4arw 4asj 4asy 4b2w 4b2x 4b3u 4b42 4b4b 4b4g 4b4m 4b5b 5fts 5ftv 5fu8 5fuh 5fye

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5FU0)