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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN RIBOKINASE IN COMPLEX WITH AMPPCP IN P21 SPACEGROUP AND WITH 4 PROTOMERS
 
Authors :  J. Park, J. Chakrabarti, B. Singh, R. S. Gupta, M. S. Junop
Date :  17 Jun 15  (Deposition) - 15 Jun 16  (Release) - 26 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
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 Amppc In P21 Spacegroup And With 4 Protomers
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RIBOKINASE
    Chains: A, B, C, D
    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

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1ACP4Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2NA8Ligand/IonSODIUM ION
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ACP2Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2NA-1Ligand/IonSODIUM ION
3PO4-1Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1ACP2Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2NA-1Ligand/IonSODIUM ION
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:199 , THR A:235 , LEU A:236 , GLY A:237 , ALA A:238 , GLY A:240 , VAL A:259 , THR A:264 , ALA A:267 , GLY A:268 , ASN A:295 , ALA A:298 , ALA A:299 , NA A:403 , HOH A:501 , HOH A:507 , HOH A:515 , HOH A:525 , HOH A:530 , HOH A:560 , HOH A:576 , HOH A:596 , HOH A:615 , HOH A:621 , HOH A:684 , HOH A:686 , HOH A:688binding site for residue ACP A 401
02AC2SOFTWAREASP A:263 , SER A:301 , ALA A:304 , SER A:310 , HOH A:579 , HOH A:629binding site for residue NA A 402
03AC3SOFTWAREACP A:401 , HOH A:501 , HOH A:513 , HOH A:530 , HOH A:569 , HOH A:615 , HOH A:655binding site for residue NA A 403
04AC4SOFTWAREASN B:199 , THR B:235 , GLY B:237 , ALA B:238 , GLY B:240 , THR B:256 , GLU B:257 , VAL B:259 , THR B:264 , THR B:265 , GLY B:266 , ALA B:267 , GLY B:268 , ASN B:295 , ALA B:298 , ALA B:299 , HOH B:510 , HOH B:542 , HOH B:543 , HOH B:548 , HOH B:572 , HOH B:573 , HOH B:577 , HOH B:637 , HOH B:644 , HOH B:659 , HOH B:663 , HOH B:671binding site for residue ACP B 401
05AC5SOFTWAREASP B:263 , SER B:301 , ALA B:304 , GLY B:306 , SER B:310 , HOH B:624binding site for residue NA B 402
06AC6SOFTWAREHOH B:523 , HOH B:536 , HOH B:542 , HOH B:612 , HOH B:641 , HOH B:663binding site for residue NA B 403
07AC7SOFTWAREASN C:199 , THR C:235 , LEU C:236 , GLY C:237 , ALA C:238 , GLY C:240 , VAL C:259 , ALA C:267 , GLY C:268 , ASN C:295 , ALA C:298 , ALA C:299 , NA C:403 , HOH C:504 , HOH C:508 , HOH C:520 , HOH C:537 , HOH C:538 , HOH C:550 , HOH C:556 , HOH C:578 , HOH C:583 , HOH C:593 , HOH C:610 , HOH C:628binding site for residue ACP C 401
08AC8SOFTWAREASP C:263 , SER C:301 , ALA C:304 , GLY C:306 , SER C:310 , HOH C:502 , HOH C:629binding site for residue NA C 402
09AC9SOFTWAREACP C:401 , HOH C:519 , HOH C:520 , HOH C:574 , HOH C:685 , HOH C:710binding site for residue NA C 403
10AD1SOFTWAREASN D:199 , THR D:235 , GLY D:237 , ALA D:238 , GLY D:240 , VAL D:259 , THR D:264 , ALA D:267 , GLY D:268 , ASN D:295 , ALA D:298 , ALA D:299 , HOH D:510 , HOH D:516 , HOH D:524 , HOH D:577 , HOH D:585binding site for residue ACP D 401
11AD2SOFTWARETYR D:282 , PRO D:283 , ASN D:284 , LEU D:285 , HOH D:547binding site for residue PO4 D 402
12AD3SOFTWAREASP D:263 , SER D:301 , ALA D:304 , SER D:310 , HOH D:581 , HOH D:594binding site for residue NA D 403
13AD4SOFTWAREHOH D:511 , HOH D:521 , HOH D:524 , HOH D:552 , HOH D:577 , HOH D:611binding site for residue NA D 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5C41)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:179 -Pro A:180
2Ala B:179 -Pro B:180
3Ala C:179 -Pro C:180
4Ala D:179 -Pro D:180

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5C41)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5C41)

(-) Exons   (0, 0)

(no "Exon" information available for 5C41)

(-) 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:317
                                                                                                                                                                                                                                                                                                                                                             
               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...hhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c41 A  14 EVAAVVVVGSCMTDLVSLTSRLPKTGETIHGHKFFIGFGGKGANQCVQAARLGAMTSMVCKVGKDSFGNDYIENLKQNDISTEFTYQTKDAATGTASIIVNNEGQNIIVIVAGANLLLNTEDLRAAANVISRAKVMVCQLEITPATSLEALTMARRSGVKTLFNPAPAIADLDPQFYTLSDVFCCNESEAEILTGLTVGSAADAGEAALVLLKRGCQVVIITLGAEGCVVLSQTEPEPKHIPTEKVKAVDTTGAGDSFVGALAFYLAYYPNLSLEDMLNRSNFIAAVSVQAAGTQSSYPYKKDLPLTLFLEHHHHHH 330
                                    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       


Chain B from PDB  Type:PROTEIN  Length:310
                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...eeeeeeee........eee..eeeeeeehhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhh......eeee.....eeeeeeee.....eeeeehhhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhh..eeee..........hhhhhh..eeeeehhhhhhhhh....hhhhhhhhhhhhhhh...eeeee.hhh.eeeee......eee...........hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c41 B  15 VAAVVVVGSCMTDLVSLTSRLPKTGETIHGHKFFIGFGGKGANQCVQAARLGAMTSMVCKVGKDSFGNDYIENLKQNDISTEFTYQTKDAATGTASIIVNNEGQNIIVIVAGANLLLNTEDLRAAANVISRAKVMVCQLEITPATSLEALTMARRSGVKTLFNPAPAIADLDPQFYTLSDVFCCNESEAEILTGLTVGSAADAGEAALVLLKRGCQVVIITLGAEGCVVLSQTEPEPKHIPTEKVKAVDTTGAGDSFVGALAFYLAYYPNLSLEDMLNRSNFIAAVSVQAAGTQSSYPYKKDLPLTLFLE 324
                                    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 C from PDB  Type:PROTEIN  Length:317
                                                                                                                                                                                                                                                                                                                                                             
               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...hhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c41 C  14 EVAAVVVVGSCMTDLVSLTSRLPKTGETIHGHKFFIGFGGKGANQCVQAARLGAMTSMVCKVGKDSFGNDYIENLKQNDISTEFTYQTKDAATGTASIIVNNEGQNIIVIVAGANLLLNTEDLRAAANVISRAKVMVCQLEITPATSLEALTMARRSGVKTLFNPAPAIADLDPQFYTLSDVFCCNESEAEILTGLTVGSAADAGEAALVLLKRGCQVVIITLGAEGCVVLSQTEPEPKHIPTEKVKAVDTTGAGDSFVGALAFYLAYYPNLSLEDMLNRSNFIAAVSVQAAGTQSSYPYKKDLPLTLFLEHHHHHH 330
                                    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       


Chain D from PDB  Type:PROTEIN  Length:316
                                                                                                                                                                                                                                                                                                                                                            
               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...hhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c41 D  14 EVAAVVVVGSCMTDLVSLTSRLPKTGETIHGHKFFIGFGGKGANQCVQAARLGAMTSMVCKVGKDSFGNDYIENLKQNDISTEFTYQTKDAATGTASIIVNNEGQNIIVIVAGANLLLNTEDLRAAANVISRAKVMVCQLEITPATSLEALTMARRSGVKTLFNPAPAIADLDPQFYTLSDVFCCNESEAEILTGLTVGSAADAGEAALVLLKRGCQVVIITLGAEGCVVLSQTEPEPKHIPTEKVKAVDTTGAGDSFVGALAFYLAYYPNLSLEDMLNRSNFIAAVSVQAAGTQSSYPYKKDLPLTLFLEHHHHH 329
                                    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)
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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  (0, 0)

(no "SCOP Domain" information available for 5C41)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5C41)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5C41)

(-) Gene Ontology  (16, 16)

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  Cis Peptide Bonds
    Ala A:179 - Pro A:180   [ RasMol ]  
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  5c41
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  RBSK_HUMAN | Q9H477
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  2.7.1.15
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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 5byf 5c3y 5c3z 5c40

(-) Related Entries Specified in the PDB File

5byc 5byd 5bye 5byf 5c3y 5c3z 5c40