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(-) Description

Title :  STRUCTURE OF THE DTDP-4-KETO-L-RHAMNOSE REDUCTASE RELATED PROTEIN (OTHER FORM) FROM THERMUS THERMOPHILUS HB8
 
Authors :  J. Jeyakanthan, S. P. Kanaujia, K. Sekar, S. Satoh, Y. Kitamura, S. Yoko S. Kuramitsu, Riken Structural Genomics/Proteomics Initiative
Date :  02 Apr 08  (Deposition) - 07 Apr 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B,C  (1x)
Biol. Unit 3:  D,E  (1x)
Keywords :  Thermus Thermophilus, Dtdp-4-Keto-L-Rhamnose Reductase, Oxidoreductase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Jeyakanthan, S. P. Kanaujia, K. Sekar, S. Satoh, Y. Kitamura, S. Yokoyama, S. Kurmamitsu
Structure Of The Dtdp-4-Keto-L-Rhamnose Reductase Related Protein (Other Form) From Thermus Thermophilus Hb8
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN TTHB138
    ChainsA, B, C, D, E
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET11A
    Expression System StrainB834(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificTHERMUS THERMOPHILUS
    Organism Taxid300852
    StrainHB8
    SynonymDTDP-4-KETO-L-RHAMNOSE REDUCTASE

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit ABCDE
Biological Unit 1 (2x)A    
Biological Unit 2 (1x) BC  
Biological Unit 3 (1x)   DE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 23)

Asymmetric Unit (5, 23)
No.NameCountTypeFull Name
1GOL11Ligand/IonGLYCEROL
2MG5Ligand/IonMAGNESIUM ION
3MSE5Mod. Amino AcidSELENOMETHIONINE
4P6G1Ligand/IonHEXAETHYLENE GLYCOL
5PG41Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION
3MSE2Mod. Amino AcidSELENOMETHIONINE
4P6G2Ligand/IonHEXAETHYLENE GLYCOL
5PG4-1Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION
3MSE2Mod. Amino AcidSELENOMETHIONINE
4P6G-1Ligand/IonHEXAETHYLENE GLYCOL
5PG4-1Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 3 (3, 6)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION
3MSE2Mod. Amino AcidSELENOMETHIONINE
4P6G-1Ligand/IonHEXAETHYLENE GLYCOL
5PG41Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:88 , ARG A:91 , HOH A:304BINDING SITE FOR RESIDUE MG A 104
02AC2SOFTWARETHR B:88 , ARG B:91 , HOH B:209 , ARG E:91BINDING SITE FOR RESIDUE MG B 104
03AC3SOFTWAREARG B:91 , THR C:88 , ARG C:91 , HOH C:205BINDING SITE FOR RESIDUE MG C 105
04AC4SOFTWAREARG C:91 , THR D:88 , ARG D:91 , PG4 E:108BINDING SITE FOR RESIDUE MG D 106
05AC5SOFTWAREARG D:91 , THR E:88 , ARG E:91 , HOH E:577BINDING SITE FOR RESIDUE MG E 107
06AC6SOFTWAREGLU A:22 , GLU A:39 , PRO A:41 , ARG A:42 , TYR A:44 , HOH A:322 , GLU B:39 , PRO B:41 , ARG B:42 , TYR B:44 , GLU C:22BINDING SITE FOR RESIDUE P6G A 105
07AC7SOFTWAREALA C:90 , MG D:106 , ALA E:90 , HOH E:484BINDING SITE FOR RESIDUE PG4 E 108
08AC8SOFTWAREVAL A:27 , VAL A:28 , GLY A:31 , LEU A:32 , ILE A:33 , LEU A:89 , ALA A:90 , HOH A:229 , HOH A:274 , HOH A:477BINDING SITE FOR RESIDUE GOL A 106
09AC9SOFTWAREARG A:46 , THR A:48 , LEU A:49 , PRO A:52 , PHE A:83 , PRO A:86 , TRP A:87 , HOH A:510BINDING SITE FOR RESIDUE GOL A 107
10BC1SOFTWAREVAL B:27 , VAL B:28 , GLY B:31 , LEU B:32 , ILE B:33 , HOH B:201 , HOH B:224 , HOH B:500 , LEU C:89 , ALA C:90BINDING SITE FOR RESIDUE GOL B 105
11BC2SOFTWARETHR B:48 , LEU B:49 , PRO B:52 , PHE B:83 , PRO B:86 , TRP B:87 , HOH B:207 , HOH B:310 , ARG E:46 , HOH E:212BINDING SITE FOR RESIDUE GOL B 106
12BC3SOFTWARETHR B:82 , PHE B:83 , GLU B:84 , PRO C:52 , GLY C:53 , PHE C:83 , HOH C:374 , HOH C:375 , HOH C:514BINDING SITE FOR RESIDUE GOL B 107
13BC4SOFTWAREVAL C:27 , VAL C:28 , GLY C:31 , ILE C:33 , HOH C:303 , HOH C:389 , HOH C:391 , LEU D:89 , ALA D:90BINDING SITE FOR RESIDUE GOL C 106
14BC5SOFTWAREARG B:46 , HOH B:361 , HOH B:379 , THR C:48 , LEU C:49 , PHE C:83 , PRO C:86 , TRP C:87 , HOH C:513BINDING SITE FOR RESIDUE GOL C 107
15BC6SOFTWAREPRO B:52 , GLY B:53 , PHE B:83 , THR C:82 , PHE C:83 , GLU C:84 , HOH C:369 , HOH C:375BINDING SITE FOR RESIDUE GOL C 108
16BC7SOFTWAREVAL D:27 , VAL D:28 , GLY D:31 , LEU D:32 , ILE D:33 , HOH D:416 , LEU E:89 , ALA E:90 , HOH E:219 , HOH E:252BINDING SITE FOR RESIDUE GOL D 107
17BC8SOFTWARELEU B:89 , ALA B:90 , VAL E:27 , VAL E:28 , GLY E:31 , LEU E:32 , ILE E:33 , HOH E:228 , HOH E:262 , HOH E:381 , HOH E:506BINDING SITE FOR RESIDUE GOL E 109
18BC9SOFTWAREARG D:46 , HOH D:222 , THR E:48 , LEU E:49 , PHE E:83 , PRO E:86 , TRP E:87 , HOH E:515 , HOH E:516BINDING SITE FOR RESIDUE GOL E 110

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:54 -A:54
2B:54 -C:54
3D:54 -E:54

(-) Cis Peptide Bonds  (11, 11)

Asymmetric Unit
No.Residues
1Pro A:40 -Pro A:41
2Glu A:84 -Pro A:85
3Pro B:40 -Pro B:41
4Glu B:84 -Pro B:85
5Asn C:5 -Pro C:6
6Pro C:40 -Pro C:41
7Glu C:84 -Pro C:85
8Pro D:40 -Pro D:41
9Glu D:84 -Pro D:85
10Pro E:40 -Pro E:41
11Glu E:84 -Pro E:85

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3CQ3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3CQ3)

(-) Exons   (0, 0)

(no "Exon" information available for 3CQ3)

(-) 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:98
 aligned with Q53W28_THET8 | Q53W28 from UniProtKB/TrEMBL  Length:103

    Alignment length:98
                                    14        24        34        44        54        64        74        84        94        
         Q53W28_THET8     5 NPLEAQAWALLEAVYDPELGLDVVNLGLIYDLVVEPPRAYVRMTLTTPGCPLHDSLGEAVRQALSRLPGVEEVEVEVTFEPPWTLARLSEKARRLLGW 102
               SCOP domains d3cq3a_ A: automated matches                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh................eeeeeee..eeeeee..........hhhhhhhhhhhh......eeeeee......hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 3cq3 A   5 NPLEAQAWALLEAVYDPELGLDVVNLGLIYDLVVEPPRAYVRmTLTTPGCPLHDSLGEAVRQALSRLPGVEEVEVEVTFEPPWTLARLSEKARRLLGW 102
                                    14        24        34        44  |     54        64        74        84        94        
                                                                     47-MSE                                                   

Chain B from PDB  Type:PROTEIN  Length:98
 aligned with Q53W28_THET8 | Q53W28 from UniProtKB/TrEMBL  Length:103

    Alignment length:98
                                    14        24        34        44        54        64        74        84        94        
         Q53W28_THET8     5 NPLEAQAWALLEAVYDPELGLDVVNLGLIYDLVVEPPRAYVRMTLTTPGCPLHDSLGEAVRQALSRLPGVEEVEVEVTFEPPWTLARLSEKARRLLGW 102
               SCOP domains d3cq3b_ B: automated matches                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh..ee....ee......eeeeeee..eeeeee..........hhhhhhhhhhhhh.....eeeeee......hhhhh..hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 3cq3 B   5 NPLEAQAWALLEAVYDPELGLDVVNLGLIYDLVVEPPRAYVRmTLTTPGCPLHDSLGEAVRQALSRLPGVEEVEVEVTFEPPWTLARLSEKARRLLGW 102
                                    14        24        34        44  |     54        64        74        84        94        
                                                                     47-MSE                                                   

Chain C from PDB  Type:PROTEIN  Length:98
 aligned with Q53W28_THET8 | Q53W28 from UniProtKB/TrEMBL  Length:103

    Alignment length:98
                                    14        24        34        44        54        64        74        84        94        
         Q53W28_THET8     5 NPLEAQAWALLEAVYDPELGLDVVNLGLIYDLVVEPPRAYVRMTLTTPGCPLHDSLGEAVRQALSRLPGVEEVEVEVTFEPPWTLARLSEKARRLLGW 102
               SCOP domains d3cq3c_ C: automated matches                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh................eeeeeee..eeeeee..........hhhhhhhhhhhhh.....eeeeee......hhhhh..hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 3cq3 C   5 NPLEAQAWALLEAVYDPELGLDVVNLGLIYDLVVEPPRAYVRmTLTTPGCPLHDSLGEAVRQALSRLPGVEEVEVEVTFEPPWTLARLSEKARRLLGW 102
                                    14        24        34        44  |     54        64        74        84        94        
                                                                     47-MSE                                                   

Chain D from PDB  Type:PROTEIN  Length:98
 aligned with Q53W28_THET8 | Q53W28 from UniProtKB/TrEMBL  Length:103

    Alignment length:98
                                    14        24        34        44        54        64        74        84        94        
         Q53W28_THET8     5 NPLEAQAWALLEAVYDPELGLDVVNLGLIYDLVVEPPRAYVRMTLTTPGCPLHDSLGEAVRQALSRLPGVEEVEVEVTFEPPWTLARLSEKARRLLGW 102
               SCOP domains d3cq3d_ D: automated matches                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.ee....ee......eeeeeee..eeeeee..........hhhhhhhhhhhhh.....eeeeee......hhhhh..hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 3cq3 D   5 NPLEAQAWALLEAVYDPELGLDVVNLGLIYDLVVEPPRAYVRmTLTTPGCPLHDSLGEAVRQALSRLPGVEEVEVEVTFEPPWTLARLSEKARRLLGW 102
                                    14        24        34        44  |     54        64        74        84        94        
                                                                     47-MSE                                                   

Chain E from PDB  Type:PROTEIN  Length:98
 aligned with Q53W28_THET8 | Q53W28 from UniProtKB/TrEMBL  Length:103

    Alignment length:98
                                    14        24        34        44        54        64        74        84        94        
         Q53W28_THET8     5 NPLEAQAWALLEAVYDPELGLDVVNLGLIYDLVVEPPRAYVRMTLTTPGCPLHDSLGEAVRQALSRLPGVEEVEVEVTFEPPWTLARLSEKARRLLGW 102
               SCOP domains d3cq3e_ E: automated matches                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh..ee....eehhhhh.eeeeeee..eeeeee..........hhhhhhhhhhhhh.....eeeeee......hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 3cq3 E   5 NPLEAQAWALLEAVYDPELGLDVVNLGLIYDLVVEPPRAYVRmTLTTPGCPLHDSLGEAVRQALSRLPGVEEVEVEVTFEPPWTLARLSEKARRLLGW 102
                                    14        24        34        44  |     54        64        74        84        94        
                                                                     47-MSE                                                   

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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  (1, 5)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3CQ3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CQ3)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3CQ3)

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 Related Entries

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

UniProtKB/TrEMBL
        Q53W28_THET8 | Q53W282cu6 3cq1 3cq2

(-) Related Entries Specified in the PDB File

2cu6
3cq1 OTHER FORM OF THIS PROTEIN
3cq2 OTHER FORM OF THIS PROTEIN RELATED ID: TTK003001362.2 RELATED DB: TARGETDB