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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 :  2.22
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
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 Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG1Ligand/IonMAGNESIUM ION
3NH41Ligand/IonAMMONIUM ION
4SO47Ligand/IonSULFATE ION
Biological Unit 1 (3, 9)
No.NameCountTypeFull Name
1GNP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3NH41Ligand/IonAMMONIUM ION
4SO47Ligand/IonSULFATE ION
Biological Unit 2 (3, 18)
No.NameCountTypeFull Name
1GNP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3NH42Ligand/IonAMMONIUM ION
4SO414Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL 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:606 , HOH A:635 , HOH A:720 , HOH A:721 , HOH A:782 , HOH A:783BINDING SITE FOR RESIDUE GNP A 501
02AC2SOFTWARETHR A:25 , THR A:62 , GNP A:501 , HOH A:720 , HOH A:721BINDING SITE FOR RESIDUE MG A 502
03AC3SOFTWAREILE A:50 , ASP A:51 , GLU A:56 , THR A:62 , ASN A:64 , HOH A:602BINDING SITE FOR RESIDUE NH4 A 503
04AC4SOFTWAREMET A:113 , PRO A:114 , ARG A:117 , HOH A:737 , HOH A:784BINDING SITE FOR RESIDUE SO4 A 504
05AC5SOFTWARELYS A:45 , HIS A:67 , HIS A:273 , ARG A:274BINDING SITE FOR RESIDUE SO4 A 505
06AC6SOFTWAREARG A:59 , HIS A:85BINDING SITE FOR RESIDUE SO4 A 506
07AC7SOFTWARELYS A:248 , ARG A:291 , HOH A:710BINDING SITE FOR RESIDUE SO4 A 507
08AC8SOFTWAREARG A:330 , HIS A:331 , THR A:332 , ARG A:393 , HOH A:763BINDING SITE FOR RESIDUE SO4 A 508
09AC9SOFTWAREARG A:57 , GLY A:358 , HOH A:634BINDING SITE FOR RESIDUE SO4 A 509
10BC1SOFTWAREGLN A:181 , ARG A:184BINDING SITE FOR RESIDUE SO4 A 510

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LC0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4LC0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LC0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LC0)

(-) Exons   (0, 0)

(no "Exon" information available for 4LC0)

(-) 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:403
                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4lc0a1 A:3-212 automated matches                                                                                                                                                                                 d4lc0a2 A:213-312 automated matches                                                                 d4lc0a3 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....eeeeee.....hhhhhhhhhhhhhh....eeeeeehhhhh.hhhhhhhhhhhhhhhhhhh........eee.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh...........eee..eeeee...eeeeeee....eee...eeeee......eeeeeeeee.......eee...eeeeee............eee.......eeeeeeeeee.hhhhh............eeee..eeeeeeee............eeeeeeeeeeee......eeeeee..eeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lc0 A   3 GEFVRTKPHVNVGTIGHVDHGKTTLTAALTYVAAAENPNVEVKDYGDIDKAPEERARGITINTAHVEYETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILVVSAADGPMPQTREHILLARQVGVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFPGDEVPVIRGSALLALEQMHRNPKTRRGENEWVDKIWELLDAIDEYIPTPVRDVDKPFLMPVEDVFTITGRGTVATGRIERGKVKVGDEVEIVGLAPETRKTVVTGVEMHRKTLQEGIAGDNVGVLLRGVSREEVERGQVLAKPGSITPHTKFEASVYVLKKEEGGRHTGFFSGYRPQFYFRTTDVTGVVQLPPGVEMVMPGDNVTFTVELIKPVALEEGLRFAIREGGRTVGAGVVTKILE 405
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402
   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 Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LC0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LC0)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

(-) Related Entries Specified in the PDB File

4lbv 4lbw 4lby 4lbz