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 COMPLEXED WITH GDPCP
 
Authors :  O. V. Kravchenko, O. S. Nikonov, V. I. Arhipova, E. A. Stolboushkina, A. G. Gabdulkhakov, A. D. Nikulin, M. B. Garber, S. V. Nikonov
Date :  09 Oct 14  (Deposition) - 11 Nov 15  (Release) - 11 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.64
Chains :  Asym./Biol. Unit :  A
Keywords :  Gamma Subunit, G-Protein, Translation, Translation Initiation, Protein Biosynthesis, Rna-Binding, Gtp-Binding, Nucleotide-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. V. Kravchenko, O. S. Nikonov, V. I. Arhipova, E. A. Stolboushkina, A. G. Gabdulkhakov, A. D. Nikulin, M. B. Garber, S. V. Nikonov
Crystal Structure Of Gamma Subunit Of The Translation Initiation Factor 2 From Sulfolobus Solfataricus In Complex With Gdpcp At 1. 64A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRANSLATION INITIATION FACTOR 2 SUBUNIT GAMMA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11D
    Expression System Strain: C41(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: EIF2G, SSO0412
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 273057
    Strain: ATCC 35092 / DSM 1617 / JCM 11322 / 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  (5, 29)

Asymmetric/Biological Unit (5, 29)
No.NameCountTypeFull Name
17PG1Ligand/Ion2,5,8,11,14,17,20,23-OCTAOXAPENTACOSAN-25-OL
2FMT23Ligand/IonFORMIC ACID
3GCP1Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
4MG2Ligand/IonMAGNESIUM ION
5NA2Ligand/IonSODIUM ION

(-) Sites  (29, 29)

Asymmetric Unit (29, 29)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:23 , THR A:46 , GCP A:527 , HOH A:604 , HOH A:921BINDING SITE FOR RESIDUE MG A 501
02AC2SOFTWAREVAL A:151 , VAL A:154 , TRP A:327 , ASN A:328 , HOH A:615 , HOH A:920BINDING SITE FOR RESIDUE MG A 502
03AC3SOFTWARETHR A:366 , LEU A:367 , ARG A:383 , ARG A:384BINDING SITE FOR RESIDUE FMT A 503
04AC4SOFTWARELEU A:312 , SER A:364 , THR A:365 , 7PG A:526 , HOH A:658 , HOH A:712BINDING SITE FOR RESIDUE FMT A 504
05AC5SOFTWAREGLN A:251 , GLU A:252 , GLU A:344 , MET A:345 , HOH A:761BINDING SITE FOR RESIDUE FMT A 505
06AC6SOFTWARELYS A:64 , TYR A:68 , LEU A:86 , FMT A:515 , HOH A:937BINDING SITE FOR RESIDUE FMT A 506
07AC7SOFTWAREPRO A:179 , ILE A:180 , HOH A:634 , HOH A:802 , HOH A:941 , HOH A:1102BINDING SITE FOR RESIDUE FMT A 507
08AC8SOFTWAREVAL A:223 , VAL A:237 , ARG A:280 , HOH A:662 , HOH A:970BINDING SITE FOR RESIDUE FMT A 508
09AC9SOFTWARELEU A:160 , TYR A:163 , ASN A:231 , HOH A:938 , HOH A:1089BINDING SITE FOR RESIDUE FMT A 509
10BC1SOFTWAREARG A:130 , HOH A:770 , HOH A:1007BINDING SITE FOR RESIDUE FMT A 510
11BC2SOFTWAREASP A:152 , VAL A:153 , HIS A:187 , PRO A:324 , LEU A:326 , GCP A:527 , HOH A:640 , HOH A:696 , HOH A:783 , HOH A:981BINDING SITE FOR RESIDUE FMT A 511
12BC3SOFTWAREILE A:32 , TYR A:51 , GLU A:53 , GLY A:282 , HOH A:760 , HOH A:880BINDING SITE FOR RESIDUE FMT A 512
13BC4SOFTWAREALA A:342 , LYS A:343 , ARG A:404 , HOH A:699 , HOH A:707 , HOH A:710BINDING SITE FOR RESIDUE FMT A 513
14BC5SOFTWARETYR A:206 , ARG A:207 , ASP A:208 , GLN A:211 , HOH A:786 , HOH A:789BINDING SITE FOR RESIDUE FMT A 514
15BC6SOFTWAREGLU A:199 , GLU A:200 , LYS A:203 , FMT A:506 , HOH A:883 , HOH A:937BINDING SITE FOR RESIDUE FMT A 515
16BC7SOFTWARETRP A:3 , ASN A:55 , PRO A:72 , FMT A:525 , HOH A:659BINDING SITE FOR RESIDUE FMT A 516
17BC8SOFTWAREILE A:32 , LYS A:36 , HOH A:836BINDING SITE FOR RESIDUE FMT A 517
18BC9SOFTWARELYS A:332 , ASN A:334 , TRP A:410 , HOH A:968BINDING SITE FOR RESIDUE FMT A 518
19CC1SOFTWARELYS A:254 , PRO A:271 , HOH A:700 , HOH A:735 , HOH A:850 , HOH A:1043BINDING SITE FOR RESIDUE FMT A 519
20CC2SOFTWARELYS A:212 , GLN A:244 , TRP A:389 , SER A:390 , HOH A:987BINDING SITE FOR RESIDUE FMT A 520
21CC3SOFTWAREPRO A:125 , GLU A:252 , HOH A:656BINDING SITE FOR RESIDUE FMT A 521
22CC4SOFTWARELYS A:347 , VAL A:348 , ASP A:349 , ARG A:399 , ILE A:401BINDING SITE FOR RESIDUE FMT A 522
23CC5SOFTWAREPRO A:205 , TYR A:206 , HOH A:998BINDING SITE FOR RESIDUE FMT A 523
24CC6SOFTWAREPHE A:286 , LYS A:287 , GLU A:288BINDING SITE FOR RESIDUE FMT A 524
25CC7SOFTWAREARG A:88 , FMT A:516 , HOH A:659 , HOH A:867BINDING SITE FOR RESIDUE FMT A 525
26CC8SOFTWAREARG A:43 , HIS A:97 , VAL A:99 , LEU A:100 , ALA A:102 , THR A:103 , THR A:365 , FMT A:504 , HOH A:862 , HOH A:932BINDING SITE FOR RESIDUE 7PG A 526
27CC9SOFTWAREVAL A:18 , ASP A:19 , HIS A:20 , GLY A:21 , LYS A:22 , THR A:23 , THR A:24 , MET A:45 , THR A:46 , GLY A:96 , ASN A:149 , LYS A:150 , ASP A:152 , VAL A:153 , SER A:184 , ALA A:185 , LEU A:186 , MG A:501 , FMT A:511 , HOH A:604 , HOH A:606 , HOH A:623 , HOH A:625 , HOH A:886 , HOH A:921 , HOH A:975 , HOH A:981 , HOH A:982 , HOH A:983BINDING SITE FOR RESIDUE GCP A 527
28DC1SOFTWARETHR A:54 , THR A:70 , HOH A:659 , HOH A:731 , HOH A:820 , HOH A:1140BINDING SITE FOR RESIDUE NA A 528
29DC2SOFTWAREMET A:111 , HOH A:627 , HOH A:673 , HOH A:704 , HOH A:727 , HOH A:732 , HOH A:1048BINDING SITE FOR RESIDUE NA A 529

(-) SS Bonds  (2, 2)

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

(-) Cis Peptide Bonds  (3, 3)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RJL)

(-) 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:414
                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeee.....hhhhhhhhhhh.....hhhhhhhh.....eeeeeeeee.........ee....hhhhh.....eeeeeeeeee...hhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhhhhh........eee.......hhhhhhhhhhhhh...........eeeeeeee.......hhhhh...eeeeeeee..ee...eeeeeeeeeeee..eeeeeeeeeeeeeeee..ee..ee.....eeeee..hhhhhhhhh....eeee......eeeeeeeeeee....................eeeeee..eeeeeeeeee...eeeeeeeeeee......eeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4rjl A   2 AWPKVQPEVNIGVVGHVDHGKTTLVQAITGIWTSKHSEELKRGMTIKLGYAETNIGVCESCKKPEAYVTEPSCKSCGSDDEPKFLRRISFIDAPGHEVLMATMLSGAALMDGAILVVAANEPFPQPQTREHFVALGIIGVKNLIIVQNKVDVVSKEEALSQYRQIKQFTKGTWAENVPIIPVSALHKINIDSLIEGIEEYIKTPYRDLSQKPVMLVIRSFDVNKPGTQFNELKGGVIGGSIIQGLFKVDQEIKVLPGLRVEKQGKVSYEPIFTKISSIRFGDEEFKEAKPGGLVAIGTYLDPSLTKADNLLGSIITLADAEVPVLWNIRIKYNLLERVVGAKEMLKVDPIRAKETLMLSVGSSTTLGIVTSVKKDEIEVELRRPVAVWSNNIRTVISRQIAGRWRMIGWGLVEI 415
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411
   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 4RJL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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
    7PG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FMT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GCP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ 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 ]
 
  Cis Peptide Bonds
    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
  4rjl
    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 4m2l 4m4s 4m53 4nbs 4qfm 4qhy 4rcy 4rcz 4rd0 4rd1 4rd2 4rd3 4rd4 4rd6 5dsz 5jb3 5jbh

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4RJL)