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(-) Description

Title :  BETA1 CARBOHYDRATE BINDING MODULE (CBM) OF AMP-ACTIVATED PROTEIN KINASE (AMPK) IN COMPLEX WITH GLUCOSYL-BETA-CYCLODODEXTRIN
 
Authors :  J. Mobbs, M. A. Gorman, M. W. Parker, P. R. Gooley, M. Griffin
Date :  24 Feb 15  (Deposition) - 24 Jun 15  (Release) - 24 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.72
Chains :  Asym. Unit :  A,B,C,D,E,F,G
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Biol. Unit 7:  G  (1x)
Keywords :  Carbohydrate Binding Module, Cbm, Ampk, Amp-Activated Protein Kinase, Cyclodextrin, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. I. Mobbs, A. Koay, A. Di Paolo, M. Bieri, E. J. Petrie, M. A. Gorman, L. Doughty, M. W. Parker, D. I. Stapleton, M. D. Griffin, P. R. Gooley
Determinants Of Oligosaccharide Specificity Of The Carbohydrate-Binding Modules Of Amp-Activated Protein Kinase.
Biochem. J. V. 468 245 2015
PubMed-ID: 25774984  |  Reference-DOI: 10.1042/BJ20150270

(-) Compounds

Molecule 1 - 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT BETA-1
    Chains: A, B, C, D, E, F, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: BL21 (DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 76-156
    Gene: PRKAB1
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: AMPKB,5'-AMP-ACTIVATED PROTEIN KINASE 40 KDA SUBUNIT

 Structural Features

(-) Chains, Units

  1234567
Asymmetric Unit : ABCDEFG
Biological Unit 1 (1x): A      
Biological Unit 2 (1x):  B     
Biological Unit 3 (1x):   C    
Biological Unit 4 (1x):    D   
Biological Unit 5 (1x):     E  
Biological Unit 6 (1x):      F 
Biological Unit 7 (1x):       G

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 16)

Asymmetric Unit (4, 16)
No.NameCountTypeFull Name
14CQ7Ligand/Ion6-O-ALPHA-D-GLUCOSYL-BETA-CYCLODEXTRIN
2GLU1Mod. Amino AcidGLUTAMIC ACID
3GOL2Ligand/IonGLYCEROL
4SO46Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
14CQ1Ligand/Ion6-O-ALPHA-D-GLUCOSYL-BETA-CYCLODEXTRIN
2GLU-1Mod. Amino AcidGLUTAMIC ACID
3GOL1Ligand/IonGLYCEROL
4SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
14CQ1Ligand/Ion6-O-ALPHA-D-GLUCOSYL-BETA-CYCLODEXTRIN
2GLU-1Mod. Amino AcidGLUTAMIC ACID
3GOL-1Ligand/IonGLYCEROL
4SO42Ligand/IonSULFATE ION
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
14CQ1Ligand/Ion6-O-ALPHA-D-GLUCOSYL-BETA-CYCLODEXTRIN
2GLU-1Mod. Amino AcidGLUTAMIC ACID
3GOL1Ligand/IonGLYCEROL
4SO4-1Ligand/IonSULFATE ION
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
14CQ1Ligand/Ion6-O-ALPHA-D-GLUCOSYL-BETA-CYCLODEXTRIN
2GLU-1Mod. Amino AcidGLUTAMIC ACID
3GOL-1Ligand/IonGLYCEROL
4SO41Ligand/IonSULFATE ION
Biological Unit 5 (2, 3)
No.NameCountTypeFull Name
14CQ1Ligand/Ion6-O-ALPHA-D-GLUCOSYL-BETA-CYCLODEXTRIN
2GLU-1Mod. Amino AcidGLUTAMIC ACID
3GOL-1Ligand/IonGLYCEROL
4SO42Ligand/IonSULFATE ION
Biological Unit 6 (2, 2)
No.NameCountTypeFull Name
14CQ1Ligand/Ion6-O-ALPHA-D-GLUCOSYL-BETA-CYCLODEXTRIN
2GLU-1Mod. Amino AcidGLUTAMIC ACID
3GOL-1Ligand/IonGLYCEROL
4SO41Ligand/IonSULFATE ION
Biological Unit 7 (2, 2)
No.NameCountTypeFull Name
14CQ1Ligand/Ion6-O-ALPHA-D-GLUCOSYL-BETA-CYCLODEXTRIN
2GLU1Mod. Amino AcidGLUTAMIC ACID
3GOL-1Ligand/IonGLYCEROL
4SO4-1Ligand/IonSULFATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:100 , LYS A:126 , TRP A:133 , SER A:144 , GLN A:145 , LEU A:146 , THR A:148 , ASN A:150 , HOH A:302 , HOH A:318 , HOH A:322 , HOH A:347 , HOH A:354 , HOH A:371 , HOH A:378 , HOH A:380 , ARG D:83 , ASN D:110 , ASN D:111 , HOH D:307binding site for residue 4CQ A 201
02AC2SOFTWARESER A:96 , PHE A:97 , GLU A:122 , HIS A:123 , HOH A:323binding site for residue GOL A 202
03AC3SOFTWARETRP B:100 , LYS B:126 , TRP B:133 , SER B:144 , GLN B:145 , LEU B:146 , THR B:148 , ASN B:150 , HOH B:304 , HOH B:331 , HOH B:347 , HOH B:371 , HOH B:393 , GLU D:122 , HOH D:303binding site for residue 4CQ B 201
04AC4SOFTWAREARG B:83 , GLN B:109 , ASN B:110 , ASN B:111 , HOH B:310 , HOH B:323 , HOH B:326 , HOH B:368 , HOH B:376 , LYS C:156binding site for residue SO4 B 202
05AC5SOFTWARELYS B:126 , TRP B:133 , THR B:134 , HIS B:135 , VAL B:149 , HOH B:304 , HOH B:388 , GLN C:109binding site for residue SO4 B 203
06AC6SOFTWARETRP C:100 , LYS C:126 , TRP C:133 , SER C:144 , GLN C:145 , THR C:148 , ASN C:150 , HOH C:304 , HOH C:307 , HOH C:308 , HOH C:316 , HOH C:321 , HOH C:349 , HOH C:352 , HOH C:357 , HOH C:359 , HOH C:371 , GLU E:122 , ARG F:83 , ASN F:110 , ASN F:111 , HOH F:305binding site for residue 4CQ C 201
07AC7SOFTWARESER C:96 , PHE C:97 , GLU C:122 , HIS C:123 , HOH C:325 , HOH C:364binding site for residue GOL C 202
08AC8SOFTWARETRP D:100 , ARG D:107 , SER D:108 , GLN D:109 , LYS D:126 , TRP D:133 , SER D:144 , GLN D:145 , LEU D:146 , THR D:148 , ASN D:150 , SO4 D:202 , HOH D:306 , HOH D:309 , HOH D:320 , HOH D:328 , ASN G:110 , 4CQ G:202binding site for residue 4CQ D 201
09AC9SOFTWAREGLN D:132 , 4CQ D:201 , HOH D:304 , HOH D:311 , HOH D:313 , HOH D:322binding site for residue SO4 D 202
10AD1SOFTWARELYS E:126 , TRP E:133 , SER E:144 , GLN E:145 , LEU E:146 , THR E:148 , ASN E:150 , HOH E:304 , HOH E:343 , HOH E:355 , HOH E:362 , HOH E:370 , HOH E:388 , HOH E:395 , GLU F:122binding site for residue 4CQ E 201
11AD2SOFTWARELYS A:156 , HOH A:307 , ARG E:83 , GLN E:109 , ASN E:110 , ASN E:111 , HOH E:329 , HOH E:336 , HOH E:373binding site for residue SO4 E 202
12AD3SOFTWAREGLN A:109 , LYS E:126 , THR E:134 , HIS E:135 , VAL E:149binding site for residue SO4 E 203
13AD4SOFTWARETRP F:100 , SER F:108 , GLN F:109 , LYS F:126 , TRP F:133 , SER F:144 , GLN F:145 , LEU F:146 , THR F:148 , ASN F:150 , SO4 F:202 , HOH F:306 , HOH F:308 , HOH F:309 , ASN G:110 , 4CQ G:202binding site for residue 4CQ F 201
14AD5SOFTWAREGLN F:132 , 4CQ F:201 , HOH F:303 , HOH F:314binding site for residue SO4 F 202
15AD6SOFTWAREPHE G:82 , LEU G:116 , ASP G:117 , LEU G:118 , GLY G:121 , HIS G:123 , ILE G:153binding site for residue GLU G 201
16AD7SOFTWARE4CQ D:201 , 4CQ F:201 , ARG G:83 , TRP G:84 , THR G:85 , GLY G:86 , GLY G:87 , GLY G:88 , LYS G:89 , ASN G:110 , ASN G:111 , PHE G:112 , LYS G:126 , PHE G:127 , PHE G:128 , VAL G:129 , ASP G:130 , GLY G:131 , GLN G:132 , TRP G:133 , THR G:134 , HIS G:135 , ASP G:136 , PRO G:137 , SER G:144 , GLN G:145 , LEU G:146 , THR G:148 , ASN G:150 , ASN G:151 , HOH G:302 , HOH G:312 , HOH G:321binding site for residue 4CQ G 202

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4YEF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YEF)

(-) 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:80
                                                                                                                
               SCOP domains -------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee......eeeee.hhh...ee.eee..eeeeee....eeeeeeeee..eee......eee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------- Transcript
                 4yef A  77 ARPTVFRWTGGGKEVYLSGSFNNWSKLPLTRSQNNFVAILDLPEGEHQYKFFVDGQWTHDPSEPIVTSQLGTVNNIIQVK 156
                                    86        96       106       116       126       136       146       156


Chain B from PDB  Type:PROTEIN  Length:86
                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhheeeeeee......eeeee.hhh...eee......eeeeeee..eeeeeeeee..eee......eee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 4yef B  71 GSPNSQARPTVFRWTGGGKEVYLSGSFNNWSKLPLTRSQNNFVAILDLPEGEHQYKFFVDGQWTHDPSEPIVTSQLGTVNNIIQVK 156
                                    80        90       100       110       120       130       140       150      


Chain C from PDB  Type:PROTEIN  Length:79
                                                                                                               
               SCOP domains ------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......eeeee.hhh...ee.eee..eeeeee....eeeeeeeee..eee......eee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                 4yef C  78 RPTVFRWTGGGKEVYLSGSFNNWSKLPLTRSQNNFVAILDLPEGEHQYKFFVDGQWTHDPSEPIVTSQLGTVNNIIQVK 156
                                    87        97       107       117       127       137       147         


Chain D from PDB  Type:PROTEIN  Length:77
                                                                                                             
               SCOP domains ----------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......eeeee.hhh...ee.eee..eeeeee....eeeeeeeee..eee......eee.....eeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                 4yef D  79 PTVFRWTGGGKEVYLSGSFNNWSKLPLTRSQNNFVAILDLPEGEHQYKFFVDGQWTHDPSEPIVTSQLGTVNNIIQV 155
                                    88        98       108       118       128       138       148       


Chain E from PDB  Type:PROTEIN  Length:85
                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhheeeeeee......eeeee.hhh...ee.......eeeeeee..eeeeeeeee..eee......eee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 4yef E  72 SPNSQARPTVFRWTGGGKEVYLSGSFNNWSKLPLTRSQNNFVAILDLPEGEHQYKFFVDGQWTHDPSEPIVTSQLGTVNNIIQVK 156
                                    81        91       101       111       121       131       141       151     


Chain F from PDB  Type:PROTEIN  Length:77
                                                                                                             
               SCOP domains ----------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......eeeee.hhh...ee.eee..eeeeee.....eeeeeeee..eee......eee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                 4yef F  79 PTVFRWTGGGKEVYLSGSFNNWSKLPLTRSQNNFVAILDLPEGEHQYKFFVDGQWTHDPSEPIVTSQLGTVNNIIQV 155
                                    88        98       108       118       128       138       148       


Chain G from PDB  Type:PROTEIN  Length:75
                                                                                                           
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......eeeee.hhh...ee.eee..eeeeee......eeeeee..eee......eee.....eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 4yef G  79 PTVFRWTGGGKEVYLSGSFNNWSKLPLTRSQNNFVAILDLPEGHQYKFFVDGQWTHDPSEPIVTSQLGTVNNIIE 201
                                    88        98       108       118  ||   129       139       149   ||
                                                                    121|                           153|
                                                                     123                            201
   Legend:   → Mismatch (orange background)
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    → 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 4YEF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

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  AAKB1_RAT | P80386
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 Related Entries

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

UniProtKB/Swiss-Prot
        AAKB1_RAT | P80386: 1z0m 1z0n 4eag 4eak 4eal 4qfg 4qfr 4qfs 5kq5 5t5t 5ufu

(-) Related Entries Specified in the PDB File

4y0g 4yee