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(-) Description

Title :  VIBRIO CHOLERAE O395 RIBOKINASE COMPLEXED WITH RIBOSE, ADP AND SODIUM ION.
 
Authors :  R. Paul, M. D. Patra, U. Sen
Date :  19 Dec 14  (Deposition) - 04 Mar 15  (Release) - 04 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Ribokinase, Ribose, Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Paul, M. D. Patra, U. Sen
Crystal Structure Of Apo And Ligand Bound Vibrio Cholerae Ribokinase (Vc-Rk): Role Of Monovalent Cation Induced Activation And Structural Flexibility In Sugar Phosphorylation
Adv. Exp. Med. Biol. V. 842 293 2015
PubMed-ID: 25408351  |  Reference-DOI: 10.1007/978-3-319-11280-0_19
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBOKINASE
    Atcc: 39541
    Chains: A, B, C, D
    EC Number: 2.7.1.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28 A(+)
    Expression System Strain: BL21 -DE3
    Expression System Taxid: 469008
    Gene: RBSK, VC0395_0007, VC395_A0124
    Organism Scientific: VIBRIO CHOLERAE SEROTYPE O1 (STRAIN ATCC 39541 / CLASSICAL OGAWA 395 / O395)
    Organism Taxid: 345073
    Strain: ATCC 39541 / CLASSICAL OGAWA 395 / O395

 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, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1ADP5Ligand/IonADENOSINE-5'-DIPHOSPHATE
2NA4Ligand/IonSODIUM ION
3RIB3Ligand/IonRIBOSE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1ADP3Ligand/IonADENOSINE-5'-DIPHOSPHATE
2NA-1Ligand/IonSODIUM ION
3RIB1Ligand/IonRIBOSE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2NA-1Ligand/IonSODIUM ION
3RIB2Ligand/IonRIBOSE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:11 , ASP A:13 , GLY A:38 , GLY A:39 , LYS A:40 , ASN A:43 , ALA A:95 , GLU A:140 , ASP A:252 , ALA A:288 , HOH A:564binding site for residue RIB A 401
02AC2SOFTWAREASN A:184 , GLY A:222 , SER A:223 , GLY A:225 , VAL A:226 , PHE A:240 , VAL A:242 , ALA A:250 , HIS A:276 , ALA A:279 , VAL A:283 , HOH A:562 , HOH A:640 , HOH A:653 , HOH A:659 , HOH A:670 , HOH A:707binding site for residue ADP A 402
03AC3SOFTWAREASP A:246 , THR A:248 , SER A:282 , ARG A:285 , SER A:291 , HOH A:565 , HOH A:568binding site for residue NA A 403
04AC4SOFTWAREASN B:184 , THR B:220 , LEU B:221 , GLY B:222 , GLY B:225 , VAL B:226 , PHE B:240 , VAL B:242 , ALA B:244 , ALA B:250 , GLY B:251 , HIS B:276 , ALA B:279 , ADP B:402 , HOH B:510 , HOH B:558 , HOH B:567 , HOH B:636 , HOH B:729binding site for residue ADP B 401
05AC5SOFTWARETHR A:27 , ASN B:11 , ASP B:13 , GLY B:38 , GLY B:39 , LYS B:40 , ASN B:43 , ILE B:109 , GLU B:140 , THR B:247 , THR B:248 , ALA B:249 , ALA B:250 , GLY B:251 , ASP B:252 , ALA B:288 , ADP B:401 , HOH B:581 , HOH B:686 , HOH B:740 , HOH B:745binding site for residue ADP B 402
06AC6SOFTWAREASP B:246 , SER B:282 , ARG B:285 , SER B:291 , HOH B:593 , HOH B:633binding site for residue NA B 403
07AC7SOFTWAREASN C:11 , ASP C:13 , GLY C:38 , GLY C:39 , LYS C:40 , ASN C:43 , ALA C:95 , GLU C:140 , THR C:248 , ASP C:252 , ALA C:288 , HOH C:547binding site for residue RIB C 401
08AC8SOFTWAREASN C:184 , THR C:220 , GLY C:222 , SER C:223 , GLY C:225 , VAL C:226 , PHE C:240 , VAL C:242 , ALA C:250 , HIS C:276 , ALA C:279 , HOH C:570 , HOH C:589 , HOH C:590 , HOH C:612 , HOH C:641 , HOH C:646 , HOH C:739binding site for residue ADP C 402
09AC9SOFTWAREASP C:246 , SER C:282 , ARG C:285 , SER C:291 , HOH C:643 , HOH C:687 , HOH C:733binding site for residue NA C 403
10AD1SOFTWAREASN D:11 , ASP D:13 , GLY D:38 , GLY D:39 , LYS D:40 , ASN D:43 , GLU D:140 , THR D:248 , ASP D:252 , HOH D:687binding site for residue RIB D 401
11AD2SOFTWAREASN D:184 , THR D:220 , LEU D:221 , GLY D:222 , SER D:223 , VAL D:226 , PHE D:240 , VAL D:242 , ALA D:250 , GLY D:251 , PHE D:254 , HIS D:276 , ALA D:279 , HOH D:594 , HOH D:605 , HOH D:643 , HOH D:669 , HOH D:681 , HOH D:683 , HOH D:686 , HOH D:691 , HOH D:747binding site for residue ADP D 402
12AD3SOFTWAREASP D:246 , SER D:282 , ARG D:285 , GLY D:287 , SER D:291binding site for residue NA D 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XDA)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:165 -Pro A:166
2Ala B:165 -Pro B:166
3Ala C:165 -Pro C:166
4Ala D:165 -Pro D:166

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XDA)

(-) 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:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee...eeeeeeee.........eeeeeeeeeeehhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhh..eeeeeeee.....eeeeeeee....eeeeeehhhhhhh....hhhhhhhhhhh.eeee....hhhhhhhhhhhhh....eeee........hhhhhh...ee..hhhhhhhhhh....hhhhhhhhhhhhhhh...eeeee.hhh.eeeee..eeeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4xda A   1 MNKLVVLGSVNADHVLQVPSFPRPGETLHGRNYQVIPGGKGANQAVAAARMQADVGFIACVGDDSFGINIRESFKLDGINTAGVKLQPNCPTGIAMIQVSDSGENSICISAEANAKLTAAAIEPDLAAIRDARYLLMQLETPLDGILKAAQEAKTAKTNVILNPAPARELPDELLKCVDLITPNETEAEVLTGITVYDDSSAQQAADALHCKGIEIVIITLGSKGVWLSQNGRGQRIPGFVVKATDTTAAGDTFNGALVTGLLQEMPLESAIKFAHAAAAISVTRFGAQTSIPTRAEVEAFLAEHS 306
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300      


Chain B from PDB  Type:PROTEIN  Length:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee...eeeeeeee.........ee.eeeeeeeehhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhh..eeeeeeee.....eeeeeeee.....eeeee.hhhhhh....hhhhhhhhhhh.eeee....hhhhhhhhhhhhhhh..eeee........hhhhhh...ee..hhhhhhhhhh....hhhhhhhhhhhhhh....eeeee.hhh.eeeee..eeeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4xda B   1 MNKLVVLGSVNADHVLQVPSFPRPGETLHGRNYQVIPGGKGANQAVAAARMQADVGFIACVGDDSFGINIRESFKLDGINTAGVKLQPNCPTGIAMIQVSDSGENSICISAEANAKLTAAAIEPDLAAIRDARYLLMQLETPLDGILKAAQEAKTAKTNVILNPAPARELPDELLKCVDLITPNETEAEVLTGITVYDDSSAQQAADALHCKGIEIVIITLGSKGVWLSQNGRGQRIPGFVVKATDTTAAGDTFNGALVTGLLQEMPLESAIKFAHAAAAISVTRFGAQTSIPTRAEVEAFLAEHS 306
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300      


Chain C from PDB  Type:PROTEIN  Length:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee...eeeeeee.........eee.eeeeeeeehhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhh..eeeeeeee.....eeeeeee.....eeeeeehhhhhhh....hhhhhhhhhhh.eeee....hhhhhhhhhhhhhh...eeee........hhhhhh...ee..hhhhhhhhhh....hhhhhhhhhhhhhh....eeeee.hhh.eeee....eeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4xda C   1 MNKLVVLGSVNADHVLQVPSFPRPGETLHGRNYQVIPGGKGANQAVAAARMQADVGFIACVGDDSFGINIRESFKLDGINTAGVKLQPNCPTGIAMIQVSDSGENSICISAEANAKLTAAAIEPDLAAIRDARYLLMQLETPLDGILKAAQEAKTAKTNVILNPAPARELPDELLKCVDLITPNETEAEVLTGITVYDDSSAQQAADALHCKGIEIVIITLGSKGVWLSQNGRGQRIPGFVVKATDTTAAGDTFNGALVTGLLQEMPLESAIKFAHAAAAISVTRFGAQTSIPTRAEVEAFLAEHS 306
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300      


Chain D from PDB  Type:PROTEIN  Length:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee...eeeeeeee.........ee.eeeeeeeehhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhhh.....eeee.....eeeeeeee....eeeeeehhhhhhh.hhhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhh..eeee........hhhhhh...ee..hhhhhhhhhh....hhhhhhhhhhhhhhh...eeeee.hhh.eeeee..eeeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4xda D   1 MNKLVVLGSVNADHVLQVPSFPRPGETLHGRNYQVIPGGKGANQAVAAARMQADVGFIACVGDDSFGINIRESFKLDGINTAGVKLQPNCPTGIAMIQVSDSGENSICISAEANAKLTAAAIEPDLAAIRDARYLLMQLETPLDGILKAAQEAKTAKTNVILNPAPARELPDELLKCVDLITPNETEAEVLTGITVYDDSSAQQAADALHCKGIEIVIITLGSKGVWLSQNGRGQRIPGFVVKATDTTAAGDTFNGALVTGLLQEMPLESAIKFAHAAAAISVTRFGAQTSIPTRAEVEAFLAEHS 306
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

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(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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  Cis Peptide Bonds
    Ala A:165 - Pro A:166   [ RasMol ]  
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  A0A0H2UL04_V | A0A0H2UL04
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 Related Entries

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

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        A0A0H2UL04_V | A0A0H2UL04: 4x8f 4xck

(-) Related Entries Specified in the PDB File

4x8f 4X8F CONTAINS THE SAME PROTEIN WITHOUT LIGAND.
4xck 4XCK CONTAINS THE SAME PROTEIN IN ADP, RIBOSE AND CESIUM ION BOUND FORM.