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(-) Description

Title :  VIBRIO CHOLERAE O395 RIBOKINASE COMPLEXED WITH ADP, RIBOSE AND CESIUM ION.
 
Authors :  R. Paul, M. D. Patra, U. Sen
Date :  18 Dec 14  (Deposition) - 21 Jan 15  (Release) - 21 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.37
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Kinase, Phosphotransfer, Sugar Binding Protein, Transferase (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 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, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1ADP5Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CS4Ligand/IonCESIUM ION
3RIB2Ligand/IonRIBOSE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1ADP3Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CS-1Ligand/IonCESIUM ION
3RIB1Ligand/IonRIBOSE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CS-1Ligand/IonCESIUM ION
3RIB1Ligand/IonRIBOSE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:11 , ASP A:13 , GLY A:38 , GLY A:39 , LYS A:40 , ASN A:43 , ALA A:95 , ILE A:109 , GLU A:140 , THR A:248 , ASP A:252 , ALA A:288binding site for residue RIB A 401
02AC2SOFTWARETHR A:220 , GLY A:222 , SER A:223 , PHE A:240 , VAL A:242 , THR A:247 , ALA A:250 , GLY A:251 , PHE A:254 , HIS A:276 , ALA A:279 , VAL A:283 , HOH A:509 , HOH A:541binding site for residue ADP A 402
03AC3SOFTWAREASP A:246 , THR A:248 , SER A:282 , ARG A:285 , GLY A:287 , SER A:291binding site for residue CS A 403
04AC4SOFTWAREASN B:184 , THR B:220 , LEU B:221 , GLY B:222 , PHE B:240 , VAL B:242 , ALA B:244 , GLY B:251 , PHE B:254 , HIS B:276 , ALA B:279 , VAL B:283 , ADP B:402 , HOH B:518 , HOH B:551binding 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:107 , ILE B:109 , GLU B:140 , THR B:247 , THR B:248 , ASP B:252 , ALA B:288 , ADP B:401 , HOH B:519binding site for residue ADP B 402
06AC6SOFTWAREASP B:246 , SER B:282 , ARG B:285 , GLY B:287 , SER B:291 , HOH B:575binding site for residue CS B 403
07AC7SOFTWAREASN C:11 , ASP C:13 , GLY C:38 , GLY C:39 , LYS C:40 , ASN C:43 , ALA C:95 , ILE C:107 , ILE C:109 , GLU C:140 , THR C:248 , ASP C:252 , ALA C:288binding 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 , GLY C:251 , HIS C:276 , ALA C:279binding site for residue ADP C 402
09AC9SOFTWAREASP C:246 , SER C:282 , ARG C:285 , GLY C:287 , SER C:291binding site for residue CS C 403
10AD1SOFTWAREASN D:184 , THR D:220 , LEU D:221 , GLY D:222 , SER D:223 , VAL D:226 , PHE D:240 , VAL D:242 , GLY D:251 , PHE D:254 , HIS D:276 , ALA D:279 , VAL D:283 , HOH D:505 , HOH D:554 , HOH D:556 , HOH D:561 , HOH D:563binding site for residue ADP D 401
11AD2SOFTWAREASP D:246 , SER D:282 , ARG D:285 , GLY D:287 , SER D:291binding site for residue CS D 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Ala A:165 -Pro A:166
2His A:305 -Ser A:306
3Ala B:165 -Pro B:166
4Ala C:165 -Pro C:166
5Ala D:165 -Pro D:166

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XCK)

(-) 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........eee.eeeeeeeehhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhh..eeeeeeee.....eeeeeeee....eeeeeehhhhhhh.hhhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhh...eeee........hhhhhh...ee..hhhhhhhhhh....hhhhhhhhhhhhhh....eeeee.hhh.eeeee...eeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4xck 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......eeee.....eeeeeeee.....eeeeehhhhhhh....hhhhhhhhhhh.eeee....hhhhhhhhhhhhhhh..eeee........hhhhhh...ee..hhhhhhhhhh....hhhhhhhhhhhhhhh...eeeee.hhh.eeeee..eeeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4xck 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.hhhhhhhhhhhhh...eeeeeeee......eeeeee.....eeeeee.hhhhhh....hhhhhhhhhhh.eeee....hhhhhhhhhhh......eeee........hhhhhhhh.ee..hhhhhhhhhh....hhhhhhhhhhhhhh....eeeee.hhh.eeeee.....ee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4xck 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.........eeeeeeeeeeehhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhh......eeee.....eeeeeeee.....eeeeehhhhhhh.hhhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhh..eeee........hhhhhh...ee..hhhhhhhhhh....hhhhhhhhhhhhhhh...eeeee.hhh.eeeee..eeeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4xck 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

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4XCK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4XCK)

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  Cis Peptide Bonds
    Ala A:165 - Pro A:166   [ RasMol ]  
    Ala B:165 - Pro B:166   [ RasMol ]  
    Ala C:165 - Pro C:166   [ RasMol ]  
    Ala D:165 - Pro D:166   [ RasMol ]  
    His A:305 - Ser A:306   [ RasMol ]  
 
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 Related Entries

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        A0A0H2UL04_V | A0A0H2UL04: 4x8f 4xda

(-) Related Entries Specified in the PDB File

4x8f 4X8F CONTAINS THE SAME PROTEIN IN APO FORM