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(-) Description

Title :  IDENTIFYING LIGAND BINDING HOT SPOTS IN PROTEINS USING BROMINATED FRAGMENTS
 
Authors :  M. K. Groftehauge, M. Therkelsen, R. Taaning, T. Skrydstrup, J. P. Mort P. Nissen
Date :  21 Jun 13  (Deposition) - 11 Sep 13  (Release) - 11 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.69
Chains :  Asym./Biol. Unit :  A
Keywords :  Gtpase, , Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. K. Grftehauge, M. O. Therkelsen, R. Taaning, T. Skrydstrup, J. P. Morth, P. Nissen
Identifying Ligand-Binding Hot Spots In Proteins Using Brominated Fragments.
Acta Crystallogr. , Sect. F V. 69 1060 2013
PubMed-ID: 23989163  |  Reference-DOI: 10.1107/S1744309113018551

(-) Compounds

Molecule 1 - ELONGATION FACTOR TU-A
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKK223-3
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TUF, TUFA
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
    Synonym: EF-TU-A

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric/Biological Unit (4, 9)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG1Ligand/IonMAGNESIUM ION
3NH41Ligand/IonAMMONIUM ION
4SO46Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:20 , ASP A:21 , HIS A:22 , GLY A:23 , LYS A:24 , THR A:25 , THR A:26 , TYR A:47 , ILE A:61 , THR A:62 , GLY A:84 , ASN A:136 , LYS A:137 , ASP A:139 , MET A:140 , SER A:174 , ALA A:175 , LEU A:176 , GLN A:354 , MG A:502 , HOH A:601 , HOH A:628 , HOH A:657 , HOH A:662BINDING SITE FOR RESIDUE GNP A 501
2AC2SOFTWARETHR A:25 , THR A:62 , GNP A:501 , HOH A:657 , HOH A:662BINDING SITE FOR RESIDUE MG A 502
3AC3SOFTWAREILE A:50 , ASP A:51 , GLU A:56 , THR A:62 , ASN A:64 , HOH A:602BINDING SITE FOR RESIDUE NH4 A 503
4AC4SOFTWAREMET A:113 , ARG A:117BINDING SITE FOR RESIDUE SO4 A 504
5AC5SOFTWAREARG A:59 , HIS A:85BINDING SITE FOR RESIDUE SO4 A 505
6AC6SOFTWARELYS A:248 , ARG A:291BINDING SITE FOR RESIDUE SO4 A 506
7AC7SOFTWAREARG A:330 , HIS A:331 , THR A:332 , ARG A:393BINDING SITE FOR RESIDUE SO4 A 507
8AC8SOFTWAREARG A:57 , GLY A:358 , HOH A:675BINDING SITE FOR RESIDUE SO4 A 508
9AC9SOFTWAREGLN A:181 , ARG A:184BINDING SITE FOR RESIDUE SO4 A 509

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LBY)

(-) 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:401
                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4lbya1 A:5-212 automated matches                                                                                                                                                                               d4lbya2 A:213-312 automated matches                                                                 d4lbya3 A:313-405 automated matches                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee.....hhhhhhhhhhhhhhhhh......hhhhhh.hhhhhhhh.....eeeeee....eeeeee...hhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhh....eeeeeehhhhh.hhhhhhhhhhhhhhhhhhh........eee.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh...........eee..eeeee...eeeeeee....eee...eeeee......eeeeeeeeee..ee..eee...eeeeee............eee.......eeeeeeeeee.hhhhh............eeee..eeeeeeee............eeeeeeeeeeee......eeeeee..eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lby A   5 FVRTKPHVNVGTIGHVDHGKTTLTAALTYVAAAENPNVEVKDYGDIDKAPEERARGITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFPGDEVPVIRGSALLALEQMHRNPKTRRGENEWVDKIWELLDAIDEYIPTPVRDVDKPFLMPVEDVFTITGRGTVATGRIERGKVKVGDEVEIVGLAPETRKTVVTGVEMHRKTLQEGIAGDNVGVLLRGVSREEVERGQVLAKPGSITPHTKFEASVYVLKKEEGGRHTGFFSGYRPQFYFRTTDVTGVVQLPPGVEMVMPGDNVTFTVELIKPVALEEGLRFAIREGGRTVGAGVVTKILE 405
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404
   Legend:   → Mismatch (orange background)
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  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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        EFTU1_THETH | P60338: 1aip 1exm 1ha3 4h9g 4lbv 4lbw 4lbz 4lc0

(-) Related Entries Specified in the PDB File

4lbv 4lbw 4lbz 4lc0