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(-) Description

Title :  CRYSTAL STRUCTURE OF THE NUCLEOTIDE-BINDING PROTEIN AF_226 IN COMPLEX WITH ADP FROM ARCHAEOGLOBUS FULGIDUS, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET GR157
 
Authors :  F. Forouhar, S. Lew, M. Abashidze, J. Seetharaman, M. Mao, R. Xiao, C. Ciccosanti, H. Wang, J. K. Everett, R. Nair, T. B. Acton, B. Rost, G. T. Montelione, J. F. Hunt, L. Tong, Northeast Structural Genomics Consortium (Nesg)
Date :  19 Oct 09  (Deposition) - 27 Oct 09  (Release) - 27 Oct 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha-Beta Protein, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Forouhar, S. Lew, M. Abashidze, J. Seetharaman, M. Mao, R. Xiao, C. Ciccosanti, H. Wang, J. K. Everett, R. Nair, T. B. Acton, B. Rost, G. T. Montelione, J. F. Hunt, L. Tong
Northeast Structural Genomics Consortium Target Gr157
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NUCLEOTIDE-BINDING PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21
    Expression System Strain: BL21(DE3)+ MAGIC
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: AF_2269
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234
    Strain: DSM 4304

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric/Biological Unit (3, 15)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MSE12Mod. Amino AcidSELENOMETHIONINE
3ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:28 , GLY A:29 , VAL A:30 , GLY A:31 , LYS A:32 , SER A:33 , THR A:34 , ASN A:190 , MSE A:191 , PRO A:227 , ILE A:228 , ASP A:229 , GLN B:163BINDING SITE FOR RESIDUE ADP A 301
2AC2SOFTWARECYS A:196 , CYS A:199 , CYS B:196 , CYS B:199BINDING SITE FOR RESIDUE ZN A 302
3AC3SOFTWAREGLN A:163 , GLY B:28 , GLY B:29 , VAL B:30 , GLY B:31 , LYS B:32 , SER B:33 , THR B:34 , ASN B:190 , MSE B:191 , PRO B:227 , ILE B:228 , ASP B:229BINDING SITE FOR RESIDUE ADP B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KB1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KB1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KB1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KB1)

(-) Exons   (0, 0)

(no "Exon" information available for 3KB1)

(-) Sequences/Alignments

Asymmetric/Biological 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:243
 aligned with O28015_ARCFU | O28015 from UniProtKB/TrEMBL  Length:254

    Alignment length:255
                                                                                                                                                                                                                                                                                    254    
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253|    
         O28015_ARCFU     4 RVTDEDIKERLDKIGFRIAVMSGKGGVGKSTVTALLAVHYAKQGKKVGILDADFLGPSIPHLFGLEKGKVAVSDEGLEPVLTQRLGIKVMSIQFLLPKRETPVIWRGPLIAGMIREFLGRVAWGELDYLLIDLPPGTGDAPLTVMQDAKPNGAVIVSTPQELTAAVVEKAITMAEQTKTAVLGIVENMAYFECPNCGERTYLFGEGKASELARKYKIEFITEIPIDSDLLKLSDLGRVEEYEPDWFEFFPY----   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh.eeeeeeeee.....hhhhhhhhhhhhhhh....eeeee......hhhhhh.......eee..eee.ee......eeee.hhh.------------hhhhhhhhhhhh.....eeeeeee......hhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhhhh..eeeeeeee..eee......eee....hhhhhhhhhhh..eeeee..hhhhhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kb1 A   4 RVTDEDIKERLDKIGFRIAVmSGKGGVGKSTVTALLAVHYAKQGKKVGILDADFLGPSIPHLFGLEKGKVAVSDEGLEPVLTQRLGIKVmSIQFLL------------LIAGmIREFLGRVAWGELDYLLIDLPPGTGDAPLTVmQDAKPNGAVIVSTPQELTAAVVEKAITmAEQTKTAVLGIVENmAYFECPNCGERTYLFGEGKASELARKYKIEFITEIPIDSDLLKLSDLGRVEEYEPDWFEFFPYLEHH 258
                                    13        23|       33        43        53        63        73        83        93     |   -       113  |    123       133       143    |  153       163       173  |    183       193       203       213       223       233       243       253     
                                               24-MSE                                                               93-MSE99          112   |                             148-MSE                     176-MSE        191-MSE                                                               
                                                                                                                                          116-MSE                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:243
 aligned with O28015_ARCFU | O28015 from UniProtKB/TrEMBL  Length:254

    Alignment length:255
                                                                                                                                                                                                                                                                                    254    
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253|    
         O28015_ARCFU     4 RVTDEDIKERLDKIGFRIAVMSGKGGVGKSTVTALLAVHYAKQGKKVGILDADFLGPSIPHLFGLEKGKVAVSDEGLEPVLTQRLGIKVMSIQFLLPKRETPVIWRGPLIAGMIREFLGRVAWGELDYLLIDLPPGTGDAPLTVMQDAKPNGAVIVSTPQELTAAVVEKAITMAEQTKTAVLGIVENMAYFECPNCGERTYLFGEGKASELARKYKIEFITEIPIDSDLLKLSDLGRVEEYEPDWFEFFPY----   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------AAA_31-3kb1B01 B:19-94                                                      ----------------------------------ParA-3kb1B03 B:129-209                                                           ------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------AAA_31-3kb1B02 B:19-94                                                      ----------------------------------ParA-3kb1B04 B:129-209                                                           ------------------------------------------------- Pfam domains (2)
         Sec.struct. author ....hhhhhhhh.eeeeeeeee.....hhhhhhhhhhhhhhh....eeeee......hhhhhh.......eee..eee.ee......eeee.hhh.------------hhhhhhhhhhhh.....eeeeeee......hhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhhhh..eeeeeeee..eee......eee....hhhhhhhhhhh..eeeee..hhhhhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kb1 B   4 RVTDEDIKERLDKIGFRIAVmSGKGGVGKSTVTALLAVHYAKQGKKVGILDADFLGPSIPHLFGLEKGKVAVSDEGLEPVLTQRLGIKVmSIQFLL------------LIAGmIREFLGRVAWGELDYLLIDLPPGTGDAPLTVmQDAKPNGAVIVSTPQELTAAVVEKAITmAEQTKTAVLGIVENmAYFECPNCGERTYLFGEGKASELARKYKIEFITEIPIDSDLLKLSDLGRVEEYEPDWFEFFPYLEHH 258
                                    13        23|       33        43        53        63        73        83        93     |   -       113  |    123       133       143    |  153       163       173  |    183       193       203       213       223       233       243       253     
                                               24-MSE                                                               93-MSE99          112   |                             148-MSE                     176-MSE        191-MSE                                                               
                                                                                                                                          116-MSE
   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 3KB1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KB1)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (O28015_ARCFU | O28015)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

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