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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN RIBOKINASE IN P21 SPACEGROUP
 
Authors :  J. Park, J. Chakrabarti, B. Singh, R. S. Gupta, M. S. Junop
Date :  10 Jun 15  (Deposition) - 15 Jun 16  (Release) - 26 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Park, J. Chakrabarti, B. Singh, R. S. Gupta, M. S. Junop
Crystal Structure Of Human Ribokinase In P21 Spacegroup
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RIBOKINASE
    Chains: A, B
    EC Number: 2.7.1.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: RBKS, RBSK
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1K1Ligand/IonPOTASSIUM ION
2NA1Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:263 , THR A:265 , SER A:301 , ALA A:304 , SER A:310 , HOH A:530 , HOH A:536binding site for residue NA A 401
2AC2SOFTWAREASP B:263 , THR B:265 , SER B:301 , ALA B:304 , GLY B:306 , SER B:310 , HOH B:506binding site for residue K B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5BYD)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:179 -Pro A:180
2Ala B:179 -Pro B:180

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5BYD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5BYD)

(-) Exons   (0, 0)

(no "Exon" information available for 5BYD)

(-) Sequences/Alignments

Asymmetric/Biological 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:315
                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...eeeeeee.........eee..eeeeeeehhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhh......eeee.....eeeeeee.....eeeeeehhhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhh..eeee..........hhhhhh..eeeeehhhhhhhhh....hhhhhhhhhhhhhhh...eeeee.hhh.eeeee......eee...........hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5byd A  15 VAAVVVVGSCMTDLVSLTSRLPKTGETIHGHKFFIGFGGKGANQCVQAARLGAMTSMVCKVGKDSFGNDYIENLKQNDISTEFTYQTKDAATGTASIIVNNEGQNIIVIVAGANLLLNTEDLRAAANVISRAKVMVCQLEITPATSLEALTMARRSGVKTLFNPAPAIADLDPQFYTLSDVFCCNESEAEILTGLTVGSAADAGEAALVLLKRGCQVVIITLGAEGCVVLSQTEPEPKHIPTEKVKAVDTTGAGDSFVGALAFYLAYYPNLSLEDMLNRSNFIAAVSVQAAGTQSSYPYKKDLPLTLFLEHHHHH 329
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324     


Chain B from PDB  Type:PROTEIN  Length:312
                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee...eeeeeee.........eee..eeeeeeehhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhh......eeee.....eeeeeee.....eeeeeehhhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhh..eeee..........hhhhhh..eeeeehhhhhhhhh....hhhhhhhhhhhhhhh...eeeee.hhh.eeeee......eee...........hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....hhhhh.hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5byd B  15 VAAVVVVGSCMTDLVSLTSRLPKTGETIHGHKFFIGFGGKGANQCVQAARLGAMTSMVCKVGKDSFGNDYIENLKQNDISTEFTYQTKDAATGTASIIVNNEGQNIIVIVAGANLLLNTEDLRAAANVISRAKVMVCQLEITPATSLEALTMARRSGVKTLFNPAPAIADLDPQFYTLSDVFCCNESEAEILTGLTVGSAADAGEAALVLLKRGCQVVIITLGAEGCVVLSQTEPEPKHIPTEKVKAVDTTGAGDSFVGALAFYLAYYPNLSLEDMLNRSNFIAAVSVQAAGTQSSYPYKKDLPLTLFLEHH 326
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324
   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 5BYD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5BYD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5BYD)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:179 - Pro A:180   [ RasMol ]  
    Ala B:179 - Pro B:180   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        RBSK_HUMAN | Q9H477: 2fv7 5byc 5bye 5byf 5c3y 5c3z 5c40 5c41

(-) Related Entries Specified in the PDB File

5byc 5bye 5byf