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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN RIBOKINASE IN COMPLEX WITH AMP
 
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 :  2.00
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 Complex With Amp
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  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2CL1Ligand/IonCHLORIDE ION
3NA4Ligand/IonSODIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:199 , THR A:235 , GLY A:237 , ALA A:238 , GLY A:240 , ALA A:267 , ASN A:295 , ALA A:298 , HOH A:507 , HOH A:515 , HOH A:516 , HOH A:548 , HOH A:593 , HOH A:595 , HOH A:637binding site for residue AMP A 401
2AC2SOFTWAREASP A:263 , SER A:301 , ALA A:304 , SER A:310 , HOH A:528 , HOH A:550binding site for residue NA A 402
3AC3SOFTWAREHOH A:517 , HOH A:539 , HOH A:558 , HOH A:593 , HOH A:613binding site for residue NA A 403
4AC4SOFTWAREASN B:199 , THR B:235 , GLY B:237 , ALA B:238 , GLY B:240 , ALA B:267 , GLY B:268 , ASN B:295 , ALA B:298 , HOH B:538binding site for residue AMP B 401
5AC5SOFTWAREASP B:263 , SER B:301 , ALA B:304 , SER B:310 , HOH B:541 , HOH B:567binding site for residue NA B 402
6AC6SOFTWAREHOH B:508 , HOH B:514 , HOH B:529 , HOH B:609 , HOH B:611binding site for residue NA B 403
7AC7SOFTWAREARG A:169 , ARG B:34binding site for residue CL B 404

(-) SS Bonds  (0, 0)

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

(-) 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 5BYF)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5BYF)

(-) 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:313
                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee...eeeeeee.........eee..eeeeeeehhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhh......eeee.....eeeeeee.....eeeeeehhhhhhhhhhhhhhhhhhhhhh.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
                 5byf A  13 EEVAAVVVVGSCMTDLVSLTSRLPKTGETIHGHKFFIGFGGKGANQCVQAARLGAMTSMVCKVGKDSFGNDYIENLKQNDISTEFTYQTKDAATGTASIIVNNEGQNIIVIVAGANLLLNTEDLRAAANVISRAKVMVCQLEITPATSLEALTMARRSGVKTLFNPAPAIADLDPQFYTLSDVFCCNESEAEILTGLTVGSAADAGEAALVLLKRGCQVVIITLGAEGCVVLSQTEPEPKHIPTEKVKAVDTTGAGDSFVGALAFYLAYYPNLSLEDMLNRSNFIAAVSVQAAGTQSSYPYKKDLPLTLFLEH 325
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322   


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.....eeeeeehhhhhhhhhhhhhhhhhhhhhh.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
                 5byf B  14 EVAAVVVVGSCMTDLVSLTSRLPKTGETIHGHKFFIGFGGKGANQCVQAARLGAMTSMVCKVGKDSFGNDYIENLKQNDISTEFTYQTKDAATGTASIIVNNEGQNIIVIVAGANLLLNTEDLRAAANVISRAKVMVCQLEITPATSLEALTMARRSGVKTLFNPAPAIADLDPQFYTLSDVFCCNESEAEILTGLTVGSAADAGEAALVLLKRGCQVVIITLGAEGCVVLSQTEPEPKHIPTEKVKAVDTTGAGDSFVGALAFYLAYYPNLSLEDMLNRSNFIAAVSVQAAGTQSSYPYKKDLPLTLFLEH 325
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323
   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 5BYF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 5byd 5bye 5c3y 5c3z 5c40 5c41

(-) Related Entries Specified in the PDB File

5byc 5byd 5bye