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(-) Description

Title :  THIT WITH LMG135 BOUND
 
Authors :  L. J. Y. M. Swier, A. Guskov, D. J. Slotboom
Date :  26 Feb 14  (Deposition) - 17 Sep 14  (Release) - 01 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  S-Component, Thiamine-Binding Protein, Ecf Module, Membrane, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. J. Swier, L. Monjas, A. Guskov, A. R. De Voogd, G. B. Erkens, D. J. Slotboom, A. K. Hirsch
Structure-Based Design Of Potent Small-Molecule Binders To The S-Component Of The Ecf Transporter For Thiamine.
Chembiochem V. 16 819 2015
PubMed-ID: 25676607  |  Reference-DOI: 10.1002/CBIC.201402673

(-) Compounds

Molecule 1 - THIAMINE TRANSPORTER THIT
    ChainsA, B
    EngineeredYES
    Expression SystemLACTOCOCCUS LACTIS
    Expression System StrainNZ9000
    Expression System Taxid1358
    FragmentTHIT
    GeneLLMG_0334, LLNZ_01755, THIT
    Organism ScientificLACTOCOCCUS LACTIS SUBSP. CREMORIS
    Organism Taxid416870
    StrainNZ9000
    SynonymTHIAMINE ECF TRANSPORTER S COMPONENT THIT

 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  (9, 37)

Asymmetric Unit (9, 37)
No.NameCountTypeFull Name
11PE3Ligand/IonPENTAETHYLENE GLYCOL
22VY2Ligand/Ion4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHENE-2-CARBALDEHYDE
3BNG6Ligand/IonB-NONYLGLUCOSIDE
4CL1Ligand/IonCHLORIDE ION
5P6G1Ligand/IonHEXAETHYLENE GLYCOL
6PEG10Ligand/IonDI(HYDROXYETHYL)ETHER
7PG02Ligand/Ion2-(2-METHOXYETHOXY)ETHANOL
8PG49Ligand/IonTETRAETHYLENE GLYCOL
9PGE3Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 1 (8, 20)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
22VY1Ligand/Ion4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHENE-2-CARBALDEHYDE
3BNG3Ligand/IonB-NONYLGLUCOSIDE
4CL-1Ligand/IonCHLORIDE ION
5P6G1Ligand/IonHEXAETHYLENE GLYCOL
6PEG5Ligand/IonDI(HYDROXYETHYL)ETHER
7PG01Ligand/Ion2-(2-METHOXYETHOXY)ETHANOL
8PG45Ligand/IonTETRAETHYLENE GLYCOL
9PGE3Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 2 (6, 16)
No.NameCountTypeFull Name
11PE2Ligand/IonPENTAETHYLENE GLYCOL
22VY1Ligand/Ion4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHENE-2-CARBALDEHYDE
3BNG3Ligand/IonB-NONYLGLUCOSIDE
4CL-1Ligand/IonCHLORIDE ION
5P6G-1Ligand/IonHEXAETHYLENE GLYCOL
6PEG5Ligand/IonDI(HYDROXYETHYL)ETHER
7PG01Ligand/Ion2-(2-METHOXYETHOXY)ETHANOL
8PG44Ligand/IonTETRAETHYLENE GLYCOL
9PGE-1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (36, 36)

Asymmetric Unit (36, 36)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:34 , GLU A:84 , TYR A:85 , TYR A:122 , HIS A:125 , GLY A:129 , TRP A:133 , TYR A:146 , ASN A:151 , HOH A:306BINDING SITE FOR RESIDUE 2VY A 201
02AC2SOFTWAREPRO A:104 , LEU A:105 , GLY A:140 , VAL A:170 , LYS A:171 , PRO A:174 , LYS A:175 , HOH A:330 , HOH A:332BINDING SITE FOR RESIDUE PG0 A 202
03AC3SOFTWARELEU A:20 , ILE A:24 , PHE A:169BINDING SITE FOR RESIDUE PG4 A 203
04AC4SOFTWARETHR A:30 , VAL A:37 , PG4 B:206BINDING SITE FOR RESIDUE PG4 A 204
05AC5SOFTWARE1PE A:216 , PG4 B:204BINDING SITE FOR RESIDUE PG4 A 206
06AC6SOFTWARESER A:25 , ASN A:29 , THR A:30 , GLY A:33 , TRP A:34 , ILE A:36 , TYR A:74 , HOH A:305 , HOH A:311BINDING SITE FOR RESIDUE PG4 A 207
07AC7SOFTWARELYS A:139 , TRP A:141 , GLY A:142 , ALA A:145BINDING SITE FOR RESIDUE BNG A 208
08AC8SOFTWAREILE A:75 , SER A:77 , LEU A:78 , LEU A:86 , BNG A:210BINDING SITE FOR RESIDUE BNG A 209
09AC9SOFTWAREILE A:65 , BNG A:209BINDING SITE FOR RESIDUE BNG A 210
10BC1SOFTWAREPHE A:22BINDING SITE FOR RESIDUE PEG A 211
11BC2SOFTWAREILE A:168BINDING SITE FOR RESIDUE PEG A 212
12BC3SOFTWAREMET A:17 , ARG A:50BINDING SITE FOR RESIDUE PEG A 213
13BC4SOFTWARELEU A:57 , VAL A:58BINDING SITE FOR RESIDUE PEG A 214
14BC5SOFTWARELYS A:106 , LEU A:107 , ALA A:108 , HOH A:326 , VAL B:31 , TYR B:32BINDING SITE FOR RESIDUE PEG A 215
15BC6SOFTWARELEU A:148 , PG4 A:206 , PG4 B:204BINDING SITE FOR RESIDUE 1PE A 216
16BC7SOFTWAREPRO A:109 , LEU A:112 , PGE A:219 , TYR B:32BINDING SITE FOR RESIDUE PGE A 217
17BC8SOFTWARELEU A:10 , THR A:54 , ARG A:99 , HOH A:316 , HOH A:317BINDING SITE FOR RESIDUE PGE A 218
18BC9SOFTWARELEU A:97 , PHE A:98 , ARG A:99 , PGE A:217 , 1PE B:215BINDING SITE FOR RESIDUE PGE A 219
19CC1SOFTWAREALA A:15BINDING SITE FOR RESIDUE P6G A 220
20CC2SOFTWARETRP B:34 , GLU B:84 , TYR B:85 , HIS B:125 , GLY B:129 , TRP B:133 , TYR B:146 , ASN B:151 , HOH B:313 , HOH B:316BINDING SITE FOR RESIDUE 2VY B 201
21CC3SOFTWARETHR B:30 , GLY B:33 , TRP B:34 , ILE B:36 , TYR B:74 , HOH B:305BINDING SITE FOR RESIDUE PG0 B 202
22CC4SOFTWARELEU B:10 , ALA B:55 , HOH B:311BINDING SITE FOR RESIDUE PG4 B 203
23CC5SOFTWAREPG4 A:206 , 1PE A:216 , LEU B:119BINDING SITE FOR RESIDUE PG4 B 204
24CC6SOFTWAREMET B:68 , ILE B:69 , PEG B:213BINDING SITE FOR RESIDUE PG4 B 205
25CC7SOFTWAREVAL A:31 , PG4 A:204 , BNG B:209BINDING SITE FOR RESIDUE PG4 B 206
26CC8SOFTWAREALA B:15 , ALA B:19 , PHE B:22 , ILE B:69BINDING SITE FOR RESIDUE BNG B 207
27CC9SOFTWARELEU B:97 , PHE B:98 , ARG B:99 , PRO B:109 , VAL B:116 , BNG B:209BINDING SITE FOR RESIDUE BNG B 208
28DC1SOFTWAREPHE B:98 , ALA B:108 , LEU B:112 , PG4 B:206 , BNG B:208BINDING SITE FOR RESIDUE BNG B 209
29DC2SOFTWAREILE B:160BINDING SITE FOR RESIDUE PEG B 210
30DC3SOFTWAREILE A:153 , LEU B:112 , PHE B:115 , PEG B:212BINDING SITE FOR RESIDUE PEG B 211
31DC4SOFTWAREPEG B:211BINDING SITE FOR RESIDUE PEG B 212
32DC5SOFTWAREMET B:68 , LEU B:78 , LEU B:86 , PG4 B:205BINDING SITE FOR RESIDUE PEG B 213
33DC6SOFTWAREPHE B:173 , PRO B:174 , LYS B:175BINDING SITE FOR RESIDUE PEG B 214
34DC7SOFTWAREPGE A:219 , LYS B:139 , GLY B:140 , TRP B:141 , ALA B:145BINDING SITE FOR RESIDUE 1PE B 215
35DC8SOFTWARETHR B:30 , ILE B:165BINDING SITE FOR RESIDUE 1PE B 216
36DC9SOFTWARETRP B:34 , TYR B:146BINDING SITE FOR RESIDUE CL B 217

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:103 -Pro A:104
2Ala B:103 -Pro B:104

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4POV)

(-) 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:178
                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh....eee..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pov A   5 KFNVRLLTEIAFMAALAFIISLIPNTVYGWIIVEIACIPILLLSLRRGLTAGLVGGLIWGILSMITGHAYILSLSQAFLEYLVAPVSLGIAGLFRQKTAPLKLAPVLLGTFVAVLLKYFFHFIAGIIFWSQYAWKGWGAVAYSLAVNGISGILTAIAAFVILIIFVKKFPKLFIHSNY 182
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174        

Chain B from PDB  Type:PROTEIN  Length:176
                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh....eee..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pov B   7 NVRLLTEIAFMAALAFIISLIPNTVYGWIIVEIACIPILLLSLRRGLTAGLVGGLIWGILSMITGHAYILSLSQAFLEYLVAPVSLGIAGLFRQKTAPLKLAPVLLGTFVAVLLKYFFHFIAGIIFWSQYAWKGWGAVAYSLAVNGISGILTAIAAFVILIIFVKKFPKLFIHSNY 182
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176      

   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 4POV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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        THIT_LACLM | A2RI474pop

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3rlb 4pop