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(-) Description

Title :  CLPB NBD2 K601Q FROM T. THERMOPHILUS IN COMPLEX WITH MANT-DADP
 
Authors :  C. Zeymer, T. R. M. Barends, N. D. Werbeck, I. Schlichting, J. Reinstein
Date :  04 Jul 13  (Deposition) - 12 Feb 14  (Release) - 09 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Aaa+ Protein, Nucleotide Binding Domain, Molecular Chaperone, Disaggregase, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Zeymer, T. R. M. Barends, N. D. Werbeck, I. Schlichting, J. Reinstei
Elements In Nucleotide Sensing And Hydrolysis Of The Aaa+ Disaggregation Machine Clpb: A Structure-Based Mechanistic Dissection Of A Molecular Motor
Acta Crystallogr. , Sect. D V. 70 582 2014
PubMed-ID: 24531492  |  Reference-DOI: 10.1107/S1399004713030629

(-) Compounds

Molecule 1 - CHAPERONE PROTEIN CLPB
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3) RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: NUCLEOTIDE BINDING DOMAIN 2, UNP RESIDUES 520-854
    Gene: CLPB
    Mutation: YES
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1MNT3Ligand/Ion2'(3')-O-N-METHYLANTHRANILOYL-ADENOSINE-5'-DIPHOSPHATE
2PO43Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1MNT1Ligand/Ion2'(3')-O-N-METHYLANTHRANILOYL-ADENOSINE-5'-DIPHOSPHATE
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1MNT1Ligand/Ion2'(3')-O-N-METHYLANTHRANILOYL-ADENOSINE-5'-DIPHOSPHATE
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1MNT1Ligand/Ion2'(3')-O-N-METHYLANTHRANILOYL-ADENOSINE-5'-DIPHOSPHATE
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:559 , VAL A:560 , VAL A:561 , GLY A:598 , VAL A:599 , GLY A:600 , GLN A:601 , THR A:602 , GLU A:603 , LEU A:757 , ILE A:765 , GLN A:769 , ALA A:805 , ARG A:806 , ARG A:809 , PO4 A:902BINDING SITE FOR RESIDUE MNT A 901
2AC2SOFTWARETHR A:597 , GLN A:601 , ASP A:667 , ASN A:709 , ARG A:806 , MNT A:901BINDING SITE FOR RESIDUE PO4 A 902
3AC3SOFTWAREARG B:559 , VAL B:560 , VAL B:561 , THR B:597 , GLY B:598 , VAL B:599 , GLY B:600 , GLN B:601 , THR B:602 , GLU B:603 , LEU B:757 , ILE B:765 , GLN B:769 , ALA B:805 , ARG B:806 , ARG B:809 , PO4 B:902BINDING SITE FOR RESIDUE MNT B 901
4AC4SOFTWARETHR B:597 , GLN B:601 , ASP B:667 , GLU B:668 , THR B:707 , ASN B:709 , ARG B:806 , MNT B:901BINDING SITE FOR RESIDUE PO4 B 902
5AC5SOFTWAREARG C:559 , VAL C:560 , VAL C:561 , THR C:597 , GLY C:598 , VAL C:599 , GLY C:600 , GLN C:601 , THR C:602 , GLU C:603 , GLN C:769 , ALA C:805 , ARG C:806 , ARG C:809BINDING SITE FOR RESIDUE MNT C 901
6AC6SOFTWARETHR C:597 , GLN C:601 , ASP C:667 , GLU C:668 , THR C:707 , ASN C:709BINDING SITE FOR RESIDUE PO4 C 902

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LJ7)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Pro B:641 -Gly B:642

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LJ7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LJ7)

(-) Exons   (0, 0)

(no "Exon" information available for 4LJ7)

(-) 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:305
                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh........eeeeee.....hhhhhhhhhhhhhhhhhh.eeeee.hhh....hhhhhhh...........hhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhheee.....eee....eeeeee..hhhhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhh...eeee....hhhhhhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh......eeeeee....eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lj7 A 545 EREKLLRLEEELHKRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGQTELAKTLAATLFDTEEAMIRIDMTEYMEKHAVSRLIGAPPGYVGYEEGGQLTEAVRRRPYSVILFDEIEKAHPDVFNILLQILDDGRLTDSHGRTVDFRNTVIILTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLNRLDEIVVFRPLTKEQIRQIVEIQLSYLRARLAEKRISLELTEAAKDFLAERGYDPVFGARPLRRVIQRELETPLAQKILAGEVKEGDRVQVDVGPAGLVFAVP 849
                                   554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844     


Chain B from PDB  Type:PROTEIN  Length:301
                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh.....hhhhhhhhhhhhhhhhh.........eeeeee.....hhhhhhhhhhhhhhhhhh.eeeee.hhh...hhhhhhhh...........hhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhh...eee.....eee....eeeeee..hhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhh...eeee....hhhhhhhhhhhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.......eeeeee....eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lj7 B 549 LLRLEEELHKRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGQTELAKTLAATLFDTEEAMIRIDMTEYMEKHAVSRLIGAPPGYVGYEEGGQLTEAVRRRPYSVILFDEIEKAHPDVFNILLQILDDGRLTDSHGRTVDFRNTVIILTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLNRLDEIVVFRPLTKEQIRQIVEIQLSYLRARLAEKRISLELTEAAKDFLAERGYDPVFGARPLRRVIQRELETPLAQKILAGEVKEGDRVQVDVGPAGLVFAVP 849
                                   558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848 


Chain C from PDB  Type:PROTEIN  Length:295
                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh.....hhhhhhhhhhhhhhhhh.........eeeeee.....hhhhhhhhhhhhhhhhhh.eeeee.hhh.hhhhhhhhh......hhhhhhhhhh...eeeee.....hhhhhhhhhhhhhh.eee.....eee....eeeeee..hhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhh...eeee....hhhhhhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh.......eeeeee....eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lj7 C 549 LLRLEEELHKRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGQTELAKTLAATLFDTEEAMIRIDMTEYMEKHAVSRLIGAPPGGGQLTEAVRRRPYSVILFDEIEKAHPDVFNILLQILDDGRLTDSHGRTVDFRNTVIILTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLNRLDEIVVFRPLTKEQIRQIVEIQLSYLRARLAEKRISLELTEAAKDFLAERGYDPVFGARPLRRVIQRELETPLAQKILAGEVKEGDRVQVDVGPAGLVFAVP 849
                                   558       568       578       588       598       608       618       628       638   ||  654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844     
                                                                                                                       642|                                                                                                                                                                                                        
                                                                                                                        649
   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 4LJ7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LJ7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LJ7)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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  4lj7
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  CLPB_THET8 | Q9RA63
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 Related Entries

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

UniProtKB/Swiss-Prot
        CLPB_THET8 | Q9RA63: 1qvr 4fct 4fcv 4fcw 4fd2 4hse 4lj4 4lj5 4lj6 4lj8 4lj9 4lja

(-) Related Entries Specified in the PDB File

4lj4 4lj5 4lj6 4lj8 4lj9 4lja