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(-) Description

Title :  STRUCTURE OF THIT WITH AV-38 BOUND
 
Authors :  L. J. Y. M. Swier, A. Guskov, D. J. Slotboom
Date :  08 Oct 13  (Deposition) - 17 Sep 14  (Release) - 17 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  S-Component, Ecf Transporter, Abc Transporter, Transport Protein, Thiamine Binding Protein-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. J. Y. M. Swier, L. Gomez, A. Guskov, A. K. H. Hirsch, D. J. Slotboom
Structural Studies On The Thiamine Binding Protein Thit
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - THIAMINE BINDING PROTEIN THIT
    Chains: A, B
    Engineered: YES
    Expression System: LACTOCOCCUS LACTIS
    Expression System Strain: NZ9000
    Expression System Taxid: 746361
    Fragment: UNP RESIDUES 7-182
    Gene: LLNZ_01755
    Organism Scientific: LACTOCOCCUS LACTIS
    Organism Taxid: 746361
    Strain: NZ9000

 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, 30)

Asymmetric Unit (9, 30)
No.NameCountTypeFull Name
11PE2Ligand/IonPENTAETHYLENE GLYCOL
2BNG5Ligand/IonB-NONYLGLUCOSIDE
3CL1Ligand/IonCHLORIDE ION
4P331Ligand/Ion3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
5PEG8Ligand/IonDI(HYDROXYETHYL)ETHER
6PG03Ligand/Ion2-(2-METHOXYETHOXY)ETHANOL
7PG42Ligand/IonTETRAETHYLENE GLYCOL
8PGE6Ligand/IonTRIETHYLENE GLYCOL
9XX82Ligand/Ion{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]PHENYL}METHANOL
Biological Unit 1 (7, 18)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2BNG3Ligand/IonB-NONYLGLUCOSIDE
3CL-1Ligand/IonCHLORIDE ION
4P33-1Ligand/Ion3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
5PEG6Ligand/IonDI(HYDROXYETHYL)ETHER
6PG02Ligand/Ion2-(2-METHOXYETHOXY)ETHANOL
7PG41Ligand/IonTETRAETHYLENE GLYCOL
8PGE4Ligand/IonTRIETHYLENE GLYCOL
9XX81Ligand/Ion{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]PHENYL}METHANOL
Biological Unit 2 (8, 11)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2BNG2Ligand/IonB-NONYLGLUCOSIDE
3CL-1Ligand/IonCHLORIDE ION
4P331Ligand/Ion3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
5PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
6PG01Ligand/Ion2-(2-METHOXYETHOXY)ETHANOL
7PG41Ligand/IonTETRAETHYLENE GLYCOL
8PGE2Ligand/IonTRIETHYLENE GLYCOL
9XX81Ligand/Ion{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]PHENYL}METHANOL

(-) Sites  (29, 29)

Asymmetric Unit (29, 29)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:34 , GLU A:84 , TYR A:122 , HIS A:125 , GLY A:129 , TRP A:133 , TYR A:146 , ASN A:151 , HOH A:301 , HOH A:309BINDING SITE FOR RESIDUE XX8 A 201
02AC2SOFTWARELEU A:97 , PHE A:98 , ARG A:99 , VAL A:116 , BNG B:202 , BNG B:203BINDING SITE FOR RESIDUE BNG A 202
03AC3SOFTWAREALA A:15BINDING SITE FOR RESIDUE BNG A 203
04AC4SOFTWAREVAL A:31 , TYR A:32 , LEU B:112 , PG4 B:207BINDING SITE FOR RESIDUE BNG A 204
05AC5SOFTWARELEU A:105 , LYS A:106 , LEU A:107 , ALA A:108 , LYS A:171 , TYR B:32BINDING SITE FOR RESIDUE PG0 A 205
06AC6SOFTWAREMET A:68 , ILE A:75 , LEU A:78 , PEG A:207BINDING SITE FOR RESIDUE PG0 A 206
07AC7SOFTWAREMET A:68 , PG0 A:206BINDING SITE FOR RESIDUE PEG A 207
08AC8SOFTWARELEU A:57BINDING SITE FOR RESIDUE PEG A 208
09AC9SOFTWAREASN A:29 , THR A:30 , GLY A:33 , TRP A:34 , ILE A:36 , TYR A:74 , PEG A:212BINDING SITE FOR RESIDUE PEG A 209
10BC1SOFTWARESER A:91 , ILE A:94 , PEG A:211BINDING SITE FOR RESIDUE PEG A 210
11BC2SOFTWAREVAL A:87 , VAL A:90 , PEG A:210BINDING SITE FOR RESIDUE PEG A 211
12BC3SOFTWARESER A:25 , ASN A:29 , TRP A:34 , ILE A:36 , GLU A:38 , ALA A:40 , PEG A:209BINDING SITE FOR RESIDUE PEG A 212
13BC4SOFTWAREASN A:29 , THR A:30 , VAL A:31 , VAL A:37BINDING SITE FOR RESIDUE PG4 A 213
14BC5SOFTWAREGLY A:140 , TRP A:141 , GLY A:142 , ALA A:145BINDING SITE FOR RESIDUE PGE A 214
15BC6SOFTWARELEU A:119 , TYR A:122 , PHE A:123 , PHE A:126 , 1PE A:218BINDING SITE FOR RESIDUE PGE A 215
16BC7SOFTWARELEU A:10 , THR A:54 , ALA A:55BINDING SITE FOR RESIDUE PGE A 217
17BC8SOFTWAREPHE A:115 , GLY A:152 , ILE A:156 , PGE A:215 , 1PE B:211BINDING SITE FOR RESIDUE 1PE A 218
18BC9SOFTWAREGLU B:84 , TYR B:122 , HIS B:125 , GLY B:129 , TRP B:133 , TYR B:146 , ASN B:151 , HOH B:301 , HOH B:303BINDING SITE FOR RESIDUE XX8 B 201
19CC1SOFTWAREBNG A:202 , LYS B:139 , GLY B:140 , TRP B:141 , BNG B:203 , PEG B:205BINDING SITE FOR RESIDUE BNG B 202
20CC2SOFTWARELEU A:107 , ALA A:108 , LEU A:112 , BNG A:202 , VAL B:31 , TYR B:32 , ILE B:35 , TRP B:138 , TRP B:141 , BNG B:202BINDING SITE FOR RESIDUE BNG B 203
21CC3SOFTWARESER B:91 , ILE B:94BINDING SITE FOR RESIDUE PG0 B 204
22CC4SOFTWAREPRO B:104 , GLY B:140 , GLY B:142 , ALA B:145 , BNG B:202BINDING SITE FOR RESIDUE PEG B 205
23CC5SOFTWAREASN B:29 , THR B:30 , GLY B:33 , TRP B:34 , ILE B:36 , TYR B:74 , HOH B:311BINDING SITE FOR RESIDUE PEG B 206
24CC6SOFTWAREBNG A:204 , LEU B:97 , ARG B:99BINDING SITE FOR RESIDUE PG4 B 207
25CC7SOFTWAREALA B:19 , ILE B:23 , PGE B:210BINDING SITE FOR RESIDUE P33 B 208
26CC8SOFTWAREMET B:68 , ILE B:69BINDING SITE FOR RESIDUE PGE B 209
27CC9SOFTWARELEU B:10 , LEU B:11 , ILE B:14 , P33 B:208 , HOH B:324BINDING SITE FOR RESIDUE PGE B 210
28DC1SOFTWARE1PE A:218 , LEU B:119 , TYR B:122 , PHE B:123 , LEU B:148BINDING SITE FOR RESIDUE 1PE B 211
29DC2SOFTWAREGLY B:33 , TRP B:34 , TRP B:138BINDING SITE FOR RESIDUE CL B 212

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4N4D)

(-) 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 4N4D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N4D)

(-) Exons   (0, 0)

(no "Exon" information available for 4N4D)

(-) 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 hhhhhhhhhhhhhhhhhhh....eee..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n4d 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: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
                 4n4d 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 4N4D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N4D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N4D)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4N4D)

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3rlb STRUCTURE OF THIT WITH NATIVE SUBSTRATE BOUND