Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  GAMMA SUBUNIT OF THE TRANSLATION INITIATION FACTOR 2 FROM SULFOLOBUS SOLFATARICUS IN NUCLEOTIDE-FREE FORM
 
Authors :  O. S. Nikonov, E. A. Stolboushkina, V. I. Arkhipova, A. G. Gabdulkhakov A. D. Nikulin, M. B. Garber, S. V. Nikonov
Date :  05 Aug 13  (Deposition) - 12 Mar 14  (Release) - 12 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A
Keywords :  Aif2, Aif2 Gamma Subunit, G-Protein, Translation, Translation Initiation, Protein Biosynthesis, Rna-Binding, Gtp-Binding, Nucleotide-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Nikonov, E. Stolboushkina, V. Arkhipova, O. Kravchenko, S. Nikonov, M. Garber
Conformational Transitions In The Gamma Subunit Of The Archaeal Translation Initiation Factor 2
Acta Crystallogr. , Sect. D V. 70 658 2014
PubMed: search  |  Reference-DOI: 10.1107/S1399004713032240

(-) Compounds

Molecule 1 - TRANSLATION INITIATION FACTOR 2 SUBUNIT GAMMA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: EIF2G
    Mutation: YES
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 273057
    Strain: P2
    Synonym: AIF2-GAMMA, EIF-2-GAMMA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 35)

Asymmetric/Biological Unit (3, 35)
No.NameCountTypeFull Name
1EDO27Ligand/Ion1,2-ETHANEDIOL
2PO44Ligand/IonPHOSPHATE ION
3SO44Ligand/IonSULFATE ION

(-) Sites  (35, 35)

Asymmetric Unit (35, 35)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:221 , ASP A:222 , LYS A:307 , ALA A:308 , HOH A:668BINDING SITE FOR RESIDUE SO4 A 501
02AC2SOFTWARELYS A:188 , ARG A:330 , GLU A:414 , HOH A:665 , HOH A:855BINDING SITE FOR RESIDUE SO4 A 502
03AC3SOFTWARELYS A:64 , TYR A:68 , LYS A:84 , HOH A:667 , HOH A:676BINDING SITE FOR RESIDUE SO4 A 503
04AC4SOFTWAREASN A:55 , ARG A:88 , HOH A:646 , HOH A:679 , HOH A:831 , HOH A:844BINDING SITE FOR RESIDUE SO4 A 504
05AC5SOFTWARELYS A:234 , SER A:277 , SER A:278 , HOH A:733 , HOH A:825BINDING SITE FOR RESIDUE PO4 A 505
06AC6SOFTWARESER A:161 , ARG A:164 , HOH A:823 , HOH A:824BINDING SITE FOR RESIDUE PO4 A 506
07AC7SOFTWARECYS A:62 , LYS A:63 , EDO A:511 , HOH A:682 , HOH A:740BINDING SITE FOR RESIDUE PO4 A 507
08AC8SOFTWARETYR A:163 , LYS A:167 , PRO A:179 , ILE A:180 , HOH A:845BINDING SITE FOR RESIDUE PO4 A 508
09AC9SOFTWAREVAL A:58 , CYS A:59 , GLU A:60 , SER A:61 , GLU A:82 , PRO A:83BINDING SITE FOR RESIDUE EDO A 509
10BC1SOFTWAREGLY A:313 , VAL A:361 , SER A:364 , VAL A:386 , ALA A:387 , TRP A:389 , HOH A:758 , HOH A:760BINDING SITE FOR RESIDUE EDO A 510
11BC2SOFTWARESER A:61 , CYS A:77 , GLY A:78 , PO4 A:507BINDING SITE FOR RESIDUE EDO A 511
12BC3SOFTWARETHR A:173 , TRP A:174BINDING SITE FOR RESIDUE EDO A 512
13BC4SOFTWAREASN A:11 , ASP A:112 , ARG A:207 , ILE A:242 , ILE A:243 , GLY A:292BINDING SITE FOR RESIDUE EDO A 513
14BC5SOFTWAREARG A:394 , HOH A:798BINDING SITE FOR RESIDUE EDO A 514
15BC6SOFTWARELYS A:212 , GLN A:244 , TRP A:389BINDING SITE FOR RESIDUE EDO A 515
16BC7SOFTWAREARG A:130 , ARG A:338BINDING SITE FOR RESIDUE EDO A 516
17BC8SOFTWARESER A:73 , LYS A:75 , SER A:76 , EDO A:518 , HOH A:686BINDING SITE FOR RESIDUE EDO A 517
18BC9SOFTWARESER A:73 , LYS A:75 , EDO A:517 , HOH A:702BINDING SITE FOR RESIDUE EDO A 518
19CC1SOFTWAREGLU A:355 , THR A:356 , HOH A:652 , HOH A:826BINDING SITE FOR RESIDUE EDO A 519
20CC2SOFTWARETHR A:46 , ARG A:280 , GLY A:282 , ALA A:296BINDING SITE FOR RESIDUE EDO A 520
21CC3SOFTWAREPRO A:182 , ASN A:190 , THR A:371 , HOH A:614 , HOH A:839BINDING SITE FOR RESIDUE EDO A 521
22CC4SOFTWAREGLN A:251 , GLU A:252 , HOH A:687BINDING SITE FOR RESIDUE EDO A 522
23CC5SOFTWAREGLY A:258 , LEU A:259 , ARG A:260 , ASN A:310 , ARG A:384BINDING SITE FOR RESIDUE EDO A 523
24CC6SOFTWARESER A:61 , LYS A:84 , HOH A:739BINDING SITE FOR RESIDUE EDO A 524
25CC7SOFTWAREASN A:391BINDING SITE FOR RESIDUE EDO A 525
26CC8SOFTWARELEU A:105 , SER A:360 , VAL A:361 , GLY A:362 , VAL A:396 , EDO A:533 , HOH A:655BINDING SITE FOR RESIDUE EDO A 526
27CC9SOFTWARECYS A:62 , LYS A:64 , HOH A:796 , HOH A:841BINDING SITE FOR RESIDUE EDO A 527
28DC1SOFTWARESER A:363 , SER A:364 , THR A:365BINDING SITE FOR RESIDUE EDO A 528
29DC2SOFTWAREILE A:32 , ALA A:52 , GLU A:53 , GLY A:282 , HOH A:806BINDING SITE FOR RESIDUE EDO A 529
30DC3SOFTWAREHIS A:17 , ASP A:19 , VAL A:118 , ALA A:119 , GLU A:122BINDING SITE FOR RESIDUE EDO A 530
31DC4SOFTWARELYS A:212 , ALA A:321 , GLU A:322BINDING SITE FOR RESIDUE EDO A 531
32DC5SOFTWAREASN A:190 , ILE A:191 , ASP A:192 , SER A:372 , LYS A:374 , GLU A:379 , HOH A:617BINDING SITE FOR RESIDUE EDO A 532
33DC6SOFTWAREALA A:108 , MET A:111 , ILE A:139 , EDO A:526 , HOH A:790BINDING SITE FOR RESIDUE EDO A 533
34DC7SOFTWAREHIS A:20 , ASN A:149 , LYS A:150 , SER A:184 , ALA A:185 , LEU A:186 , HOH A:662BINDING SITE FOR RESIDUE EDO A 534
35DC8SOFTWAREGLN A:400 , ALA A:402BINDING SITE FOR RESIDUE EDO A 535

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:59 -A:74
2A:62 -A:77

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Lys A:64 -Pro A:65
2Phe A:124 -Pro A:125
3Leu A:256 -Pro A:257
4Ala A:342 -Lys A:343

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M2L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M2L)

(-) Exons   (0, 0)

(no "Exon" information available for 4M2L)

(-) 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:398
                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4m2la1 A:2-206 Initiation factor eIF2 gamma subunit, N-terminal (G) domain                                                                                                                  d4m2la2 A:207-320 Initiation factor eIF2 gamma subunit, domain II                                                 d4m2la3 A:321-415 Initiation factor eIF2 gamma subunit                                          SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeee....hhhhhhhhhhh......eeeeeeee.........ee....hhhhh.....eeeeeeeeee...hhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhhhhhhh........eee.......hhhhhhhhhhhhh...........eeeeeeee.......hhhhh...eeeeeeee..ee...eeeeeeeeee......eeeeeeeeeeeeee..eee.ee.....eeeee..hhhhhhhhh....eeee......eeeeeeeeeee..ee......ee........eeeeee..eeeeeeeeee...eeeeeeeeeee.......eeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m2l A   2 AWPKVQPEVNIGVVGHVDHGKTTLVQAITGITIKLGYAETNIGVCESCKKPEAYVTEPSCKSCGSDDEPKFLRRISFIDAPVLMATMLSGAALMDGAILVVAANEPFPQPQTREHFVALGIIGVKNLIIVQNKVDVVSKEEALSQYRQIKQFTKGTWAENVPIIPVSALHKINIDSLIEGIEEYIKTPYRDLSQKPVMLVIRSFDVNKPGTQFNELKGGVIGGSIIQGLFKVDQEIKVLPGLRVEKQGKVSYEPIFTKISSIRFGDEEFKEAKPGGLVAIGTYLDPSLTKADNLLGSIITLADAEVPVLWNIRIKYNLLERVVGAKEMLKVDPIRAKETLMLSVGSSTTLGIVTSVKKDEIEVELRRPVAVWSNNIRTVISRQIAGRWRMIGWGLVEI 415
                                    11        21        31||      54        64        74        84        94||     107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407        
                                                         32|                                               95|                                                                                                                                                                                                                                                                                                                            
                                                          46                                                99
   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  (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 4M2L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M2L)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
    CC3  [ RasMol ]  +environment [ RasMol ]
    CC4  [ RasMol ]  +environment [ RasMol ]
    CC5  [ RasMol ]  +environment [ RasMol ]
    CC6  [ RasMol ]  +environment [ RasMol ]
    CC7  [ RasMol ]  +environment [ RasMol ]
    CC8  [ RasMol ]  +environment [ RasMol ]
    CC9  [ RasMol ]  +environment [ RasMol ]
    DC1  [ RasMol ]  +environment [ RasMol ]
    DC2  [ RasMol ]  +environment [ RasMol ]
    DC3  [ RasMol ]  +environment [ RasMol ]
    DC4  [ RasMol ]  +environment [ RasMol ]
    DC5  [ RasMol ]  +environment [ RasMol ]
    DC6  [ RasMol ]  +environment [ RasMol ]
    DC7  [ RasMol ]  +environment [ RasMol ]
    DC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:342 - Lys A:343   [ RasMol ]  
    Leu A:256 - Pro A:257   [ RasMol ]  
    Lys A:64 - Pro A:65   [ RasMol ]  
    Phe A:124 - Pro A:125   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4m2l
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  IF2G_SULSO | Q980A5
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  IF2G_SULSO | Q980A5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        IF2G_SULSO | Q980A5: 2aho 2plf 2pmd 2qmu 2qn6 3cw2 3i1f 3pen 3qsy 3sjz 3v11 4m0l 4m4s 4m53 4nbs 4qfm 4qhy 4rcy 4rcz 4rd0 4rd1 4rd2 4rd3 4rd4 4rd6 4rjl 5dsz 5jb3 5jbh

(-) Related Entries Specified in the PDB File

4m0l 4m4s 4m53