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(-) Description

Title :  HUMAN PEROXIREDOXIN-1 C83S MUTANT
 
Authors :  K. J. Cho, J. -H. Lee, T. G. Khan, Y. Park, A. Cho, T. -S. Chang, K. H. Kim
Date :  18 Dec 14  (Deposition) - 13 Jan 16  (Release) - 05 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Peroxiredoxin, C83S Mutant, Helix-To-Loop Conformational Transition, Chaps, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. J. Cho, Y. Park, T. G. Khan, J. -H. Lee, S. Kim, J. H. Seok, Y. B. Chung, A. E. Cho, Y. Choi, T. -S. Chang, K. H. Kim
Crystal Structure Of Dimeric Human Peroxiredoxin-1 C83S Mutant
Bull. Korean Chem. Soc. V. 36 1543 2015
PubMed: search  |  Reference-DOI: 10.1002/BKCS.10284

(-) Compounds

Molecule 1 - PEROXIREDOXIN-1
    Chains: A, B, C, D, E, F
    EC Number: 1.11.1.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PRDX1, PAGA, PAGB, TDPX2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NATURAL KILLER CELL-ENHANCING FACTOR A,NKEF-A,PROLIFERATION- ASSOCIATED GENE PROTEIN,PAG,THIOREDOXIN PEROXIDASE 2,THIOREDOXIN- DEPENDENT PEROXIDE REDUCTASE 2

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):   CD  
Biological Unit 3 (1x):     EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1CPS3Ligand/Ion3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
2GOL3Ligand/IonGLYCEROL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CPS1Ligand/Ion3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
2GOL1Ligand/IonGLYCEROL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CPS1Ligand/Ion3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
2GOL1Ligand/IonGLYCEROL
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1CPS1Ligand/Ion3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE
2GOL1Ligand/IonGLYCEROL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:128 , LEU A:130 , THR A:143 , ASN A:145 , ARG A:151 , HOH A:333 , HOH A:357binding site for residue GOL A 201
2AC2SOFTWARETHR A:90 , LYS A:92 , LYS A:93 , GLY A:95 , HOH A:356 , GLY B:176 , TRP B:177 , LYS B:178 , PRO B:179 , HOH B:217binding site for residue CPS A 202
3AC3SOFTWAREARG C:128 , LEU C:130 , THR C:143 , ASN C:145 , ARG C:151 , HOH C:345 , HOH C:378binding site for residue GOL C 201
4AC4SOFTWARETRP C:87 , THR C:90 , LYS C:92 , LYS C:93 , GLN C:94 , GLY C:95 , HOH C:310 , GLY D:176 , TRP D:177 , LYS D:178 , HOH D:325 , HOH D:337 , LYS E:109binding site for residue CPS D 201
5AC5SOFTWAREGLY E:176 , TRP E:177 , LYS E:178 , PRO E:179 , HOH E:304 , HOH E:314 , HOH E:338 , THR F:90 , LYS F:92 , LYS F:93 , GLY F:95binding site for residue CPS E 201
6AC6SOFTWAREARG F:128 , GLY F:129 , LEU F:130 , ASN F:145 , ARG F:151 , HOH F:326 , HOH F:344binding site for residue GOL F 201

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:52 -B:173
2A:173 -B:52
3C:52 -D:173
4C:173 -D:52
5E:52 -F:173
6E:173 -F:52

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4XCS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XCS)

(-) 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:179
                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eeeee.....eeeee.hhhh..eeeeeee..hhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhh.hhhhh........eee...hhhhhhh...........eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xcs A  -2 GSHMSSGNAKIGHPAPNFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVCPTEIIAFSDRAEEFKKLNCQVIGASVDSHFSHLAWVNTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITVNDLPVGRSVDETLRLVQAFQFTDKHGEVCPAG 176
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167         


Chain B from PDB  Type:PROTEIN  Length:176
                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee.....eeeee.hhhh..eeeeee.........hhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhh.hhhhh........eee...hhhhhhh..ee....ee.eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xcs B   4 GNAKIGHPAPNFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVCPTEIIAFSDRAEEFKKLNCQVIGASVDSHFSHLAWVNTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITVNDLPVGRSVDETLRLVQAFQFTDKHGEVCPAGWKP 179
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173      


Chain C from PDB  Type:PROTEIN  Length:179
                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eeeee.....eeeee.hhhh..eeeeeee..hhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhh.hhhhh........eee...hhhhhhh...........eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xcs C  -2 GSHMSSGNAKIGHPAPNFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVCPTEIIAFSDRAEEFKKLNCQVIGASVDSHFSHLAWVNTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITVNDLPVGRSVDETLRLVQAFQFTDKHGEVCPAG 176
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167         


Chain D from PDB  Type:PROTEIN  Length:176
                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee.....eeeee.hhhh..eeeeee.........hhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhh.hhhhh........eee...hhhhhhh...........eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xcs D   4 GNAKIGHPAPNFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVCPTEIIAFSDRAEEFKKLNCQVIGASVDSHFSHLAWVNTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITVNDLPVGRSVDETLRLVQAFQFTDKHGEVCPAGWKP 179
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173      


Chain E from PDB  Type:PROTEIN  Length:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee.....eeeee.hhhh..eeeeee........hhhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhh..............eee...hhhhhhh...........eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xcs E   3 SGNAKIGHPAPNFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVCPTEIIAFSDRAEEFKKLNCQVIGASVDSHFSHLAWVNTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITVNDLPVGRSVDETLRLVQAFQFTDKHGEVCPAGWKP 179
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       


Chain F from PDB  Type:PROTEIN  Length:179
                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eeeee.....eeeee.hhhh..eeeeeee..hhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhh.hhhhh........eee...hhhhhhh...........eeeeee.....eeeeeee......hhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xcs F  -2 GSHMSSGNAKIGHPAPNFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVCPTEIIAFSDRAEEFKKLNCQVIGASVDSHFSHLAWVNTPKKQGGLGPMNIPLVSDPKRTIAQDYGVLKADEGISFRGLFIIDDKGILRQITVNDLPVGRSVDETLRLVQAFQFTDKHGEVCPAG 176
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167
   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 4XCS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (27, 27)

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        PRDX1_HUMAN | Q06830: 2rii 3hy2

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