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(-) Description

Title :  CRYSTAL STRUCTURE OF THIT COMPLEXED WITH LMG116
 
Authors :  L. J. Y. M. Swier, A. Guskov, D. J. Slotboom
Date :  27 Aug 13  (Deposition) - 27 Aug 14  (Release) - 27 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  S-Component, Ecf Transporter, Abc Transporter, Thiamine Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. J. Y. M. Swier, L. Gomez, A. Guskov, A. K. H. Hirsch, D. J. Slotboom
Crystal Structures Of Thit With Small Molecule Modulators
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - THIAMINE TRANSPORTER THIT
    Chains: A, B
    Engineered: YES
    Expression System: LACTOCOCCUS LACTIS
    Expression System Strain: NZ9000
    Expression System Taxid: 746361
    Gene: LLNZ_01755, THIT
    Organism Scientific: LACTOCOCCUS LACTIS SUBSP. CREMORIS
    Organism Taxid: 746361
    Strain: NZ9000
    Synonym: THIAMINE 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  (7, 47)

Asymmetric Unit (7, 47)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
226G2Ligand/Ion2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]PHENYL}ETHANOL
3BNG7Ligand/IonB-NONYLGLUCOSIDE
4P6G7Ligand/IonHEXAETHYLENE GLYCOL
5PEG17Ligand/IonDI(HYDROXYETHYL)ETHER
6PG02Ligand/Ion2-(2-METHOXYETHOXY)ETHANOL
7PG411Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 1 (6, 21)
No.NameCountTypeFull Name
11PE-1Ligand/IonPENTAETHYLENE GLYCOL
226G1Ligand/Ion2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]PHENYL}ETHANOL
3BNG2Ligand/IonB-NONYLGLUCOSIDE
4P6G4Ligand/IonHEXAETHYLENE GLYCOL
5PEG5Ligand/IonDI(HYDROXYETHYL)ETHER
6PG01Ligand/Ion2-(2-METHOXYETHOXY)ETHANOL
7PG48Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 2 (7, 26)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
226G1Ligand/Ion2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]PHENYL}ETHANOL
3BNG5Ligand/IonB-NONYLGLUCOSIDE
4P6G3Ligand/IonHEXAETHYLENE GLYCOL
5PEG12Ligand/IonDI(HYDROXYETHYL)ETHER
6PG01Ligand/Ion2-(2-METHOXYETHOXY)ETHANOL
7PG43Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (47, 47)

Asymmetric Unit (47, 47)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:360BINDING SITE FOR RESIDUE BNG A 201
02AC2SOFTWAREILE A:94 , LEU A:97 , PHE A:98 , VAL A:116 , HOH A:345 , BNG B:201 , BNG B:202BINDING SITE FOR RESIDUE BNG A 202
03AC3SOFTWAREGLU A:38 , GLU A:84 , TYR A:85 , HIS A:125 , GLY A:129 , TRP A:133 , TYR A:146 , ASN A:151 , PG4 A:210 , HOH A:312 , HOH A:322 , HOH A:336BINDING SITE FOR RESIDUE 26G A 203
04AC4SOFTWAREVAL A:37 , LEU A:157 , ALA A:161 , PG4 A:208 , LEU B:111BINDING SITE FOR RESIDUE PG4 A 204
05AC5SOFTWARELEU A:119 , TYR A:122 , P6G A:221BINDING SITE FOR RESIDUE PG4 A 205
06AC6SOFTWAREVAL A:164 , ILE A:167 , ILE A:168 , LYS A:172 , VAL B:164BINDING SITE FOR RESIDUE PG4 A 206
07AC7SOFTWARESER A:91 , ILE A:94BINDING SITE FOR RESIDUE PG4 A 207
08AC8SOFTWARETHR A:30 , VAL A:31 , PG4 A:204BINDING SITE FOR RESIDUE PG4 A 208
09AC9SOFTWARETRP A:141 , PG0 A:217 , HOH A:367 , HOH A:368BINDING SITE FOR RESIDUE PG4 A 209
10BC1SOFTWAREASN A:29 , THR A:30 , GLY A:33 , TRP A:34 , ILE A:36 , TYR A:74 , 26G A:203 , HOH A:322 , HOH A:366 , HOH A:370BINDING SITE FOR RESIDUE PG4 A 210
11BC2SOFTWARELEU A:10 , LEU A:11 , ARG A:51 , THR A:54 , ARG A:99 , HIS A:179 , HOH A:307 , HOH A:342BINDING SITE FOR RESIDUE PG4 A 211
12BC3SOFTWAREVAL A:90BINDING SITE FOR RESIDUE PEG A 212
13BC4SOFTWARELEU A:105 , LYS A:106 , LEU A:107 , ALA A:108 , LYS A:171 , TYR B:32BINDING SITE FOR RESIDUE PEG A 213
14BC5SOFTWARETRP A:138 , P6G A:221 , PEG B:212BINDING SITE FOR RESIDUE PEG A 214
15BC6SOFTWAREVAL A:31 , ILE A:153 , LEU B:112 , BNG B:205 , PEG B:212BINDING SITE FOR RESIDUE PEG A 215
16BC7SOFTWARETYR A:136 , TYR A:182BINDING SITE FOR RESIDUE PEG A 216
17BC8SOFTWAREGLY A:142 , ALA A:143 , VAL A:144 , ALA A:145 , PG4 A:209 , HOH A:313 , HOH A:338 , HOH A:352BINDING SITE FOR RESIDUE PG0 A 217
18BC9SOFTWAREILE A:75 , LEU A:78 , P6G A:219BINDING SITE FOR RESIDUE P6G A 218
19CC1SOFTWAREILE A:69 , THR A:70 , GLY A:71 , P6G A:218BINDING SITE FOR RESIDUE P6G A 219
20CC2SOFTWARELEU A:20 , ILE A:24 , ILE A:42 , LEU A:46 , PHE A:169 , LEU A:176BINDING SITE FOR RESIDUE P6G A 220
21CC3SOFTWAREPHE A:115 , TRP A:141 , ALA A:145 , LEU A:148 , ILE A:156 , PG4 A:205 , PEG A:214 , PEG B:217 , P6G B:225BINDING SITE FOR RESIDUE P6G A 221
22CC4SOFTWAREALA A:108 , LEU A:112 , BNG A:202 , VAL B:31 , TYR B:32 , ILE B:35 , TRP B:138 , HOH B:331 , HOH B:341 , HOH B:379BINDING SITE FOR RESIDUE BNG B 201
23CC5SOFTWARELEU A:119 , BNG A:202 , LYS B:139 , GLY B:140 , TRP B:141 , ALA B:145 , PEG B:215 , HOH B:341 , HOH B:375 , HOH B:380BINDING SITE FOR RESIDUE BNG B 202
24CC6SOFTWAREPHE B:22 , ILE B:69 , 1PE B:222 , HOH B:376 , HOH B:377BINDING SITE FOR RESIDUE BNG B 203
25CC7SOFTWARELEU B:97 , PHE B:98 , PRO B:109 , VAL B:116 , BNG B:205 , HOH B:323 , HOH B:378BINDING SITE FOR RESIDUE BNG B 204
26CC8SOFTWAREPEG A:215 , PHE B:98 , LEU B:112 , BNG B:204 , HOH B:388 , HOH B:389BINDING SITE FOR RESIDUE BNG B 205
27CC9SOFTWAREGLU B:38 , GLU B:84 , TYR B:85 , HIS B:125 , GLY B:129 , TRP B:133 , TYR B:146 , ASN B:151 , PG4 B:209 , HOH B:307 , HOH B:308 , HOH B:335BINDING SITE FOR RESIDUE 26G B 206
28DC1SOFTWARETHR B:54 , LEU B:57BINDING SITE FOR RESIDUE PG4 B 207
29DC2SOFTWAREPHE B:163 , ILE B:167 , LYS B:171BINDING SITE FOR RESIDUE PG4 B 208
30DC3SOFTWARETHR B:30 , GLY B:33 , TRP B:34 , ILE B:36 , TYR B:74 , 26G B:206 , PEG B:211 , HOH B:352BINDING SITE FOR RESIDUE PG4 B 209
31DC4SOFTWARELEU B:78 , PHE B:82 , LEU B:86 , 1PE B:222BINDING SITE FOR RESIDUE PEG B 210
32DC5SOFTWARETYR B:74 , LEU B:76 , TYR B:136 , PG4 B:209BINDING SITE FOR RESIDUE PEG B 211
33DC6SOFTWAREPEG A:214 , PEG A:215 , LEU B:112 , VAL B:116BINDING SITE FOR RESIDUE PEG B 212
34DC7SOFTWAREP6G B:226BINDING SITE FOR RESIDUE PEG B 213
35DC8SOFTWAREASN B:29 , P6G B:226BINDING SITE FOR RESIDUE PEG B 214
36DC9SOFTWAREBNG B:202BINDING SITE FOR RESIDUE PEG B 215
37EC1SOFTWAREPHE B:173 , PRO B:174 , LYS B:175 , PEG B:218BINDING SITE FOR RESIDUE PEG B 216
38EC2SOFTWAREP6G A:221 , LEU B:119 , P6G B:225BINDING SITE FOR RESIDUE PEG B 217
39EC3SOFTWAREPHE B:173 , PEG B:216 , P6G B:226BINDING SITE FOR RESIDUE PEG B 218
40EC4SOFTWAREILE B:131 , PEG B:220BINDING SITE FOR RESIDUE PEG B 219
41EC5SOFTWAREILE B:130 , PEG B:219 , HOH B:337BINDING SITE FOR RESIDUE PEG B 220
42EC6SOFTWARELEU B:11 , THR B:54BINDING SITE FOR RESIDUE PEG B 221
43EC7SOFTWAREMET B:68 , ILE B:69 , THR B:70 , BNG B:203 , PEG B:210BINDING SITE FOR RESIDUE 1PE B 222
44EC8SOFTWAREILE B:23 , LEU B:26BINDING SITE FOR RESIDUE PG0 B 223
45EC9SOFTWAREVAL B:87 , VAL B:90BINDING SITE FOR RESIDUE P6G B 224
46FC1SOFTWARELEU A:148 , P6G A:221 , LEU B:119 , PHE B:123 , PHE B:126 , LEU B:148 , PEG B:217BINDING SITE FOR RESIDUE P6G B 225
47FC2SOFTWAREILE B:24 , LEU B:46 , PHE B:169 , PEG B:213 , PEG B:214 , PEG B:218BINDING SITE FOR RESIDUE P6G B 226

(-) SS Bonds  (0, 0)

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

(-) 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 4MES)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MES)

(-) 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:176
                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh...eee..ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mes A   7 NVRLLTEIAFMAALAFIISLIPNTVYGWIIVEIACIPILLLSLRRGLTAGLVGGLIWGILSMITGHAYILSLSQAFLEYLVAPVSLGIAGLFRQKTAPLKLAPVLLGTFVAVLLKYFFHFIAGIIFWSQYAWKGWGAVAYSLAVNGISGILTAIAAFVILIIFVKKFPKLFIHSNY 182
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176      


Chain B from PDB  Type:PROTEIN  Length:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh....eee..ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mes B   6 FNVRLLTEIAFMAALAFIISLIPNTVYGWIIVEIACIPILLLSLRRGLTAGLVGGLIWGILSMITGHAYILSLSQAFLEYLVAPVSLGIAGLFRQKTAPLKLAPVLLGTFVAVLLKYFFHFIAGIIFWSQYAWKGWGAVAYSLAVNGISGILTAIAAFVILIIFVKKFPKLFIHSNY 182
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175
   Legend:   → Mismatch (orange background)
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  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 4MES)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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3rlb STRUCTURE OF THIT WITH NATIVE SUBSTRATE BOUND