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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF TTK003000868 FROM THERMUS THERMOPHILUS HB8

Authors :   H. Wang, C. Takemoto-Hori, K. Murayama, S. Sekine, T. Terada, M. Shirouzu, S. Kuramitsu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   17 May 04 (Deposition) - 17 May 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A

Keywords :   Gtp Complex, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Wang, C. Takemoto-Hori, K. Murayama, S. Sekine, T. Terada, M. Shirouzu, S. Kuramitsu, S. Yokoyama
Crystal Structure Of Ttk003000868 From Thermus Thermophilus Hb8
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - ELONGATION FACTOR G HOMOLOG
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274
	Synonym	:	EF-G-2

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	GTP	1	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
2	MG	1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:23 , THR A:61 , GTP A:700 , HOH A:702 , HOH A:703	BINDING SITE FOR RESIDUE MG A 701
2	AC2	SOFTWARE	ALA A:18 , GLY A:19 , SER A:20 , GLY A:21 , LYS A:22 , THR A:23 , THR A:24 , VAL A:42 , GLU A:43 , THR A:60 , THR A:61 , GLY A:83 , LYS A:135 , ASP A:137 , LYS A:138 , SER A:254 , GLU A:256 , MG A:701 , HOH A:702 , HOH A:753 , HOH A:903	BINDING SITE FOR RESIDUE GTP A 700

(no "SS Bond" information available for 1WDT)

(no "Cis Peptide Bond" information available for 1WDT)

(no "SAP(SNP)/Variant" information available for 1WDT)

(no "PROSITE Motif" information available for 1WDT)

(no "Exon" information available for 1WDT)

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
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Chain A from PDB  Type:PROTEIN  Length:660
 aligned with Q5SI76_THET8 | Q5SI76 from UniProtKB/TrEMBL  Length:658

    Alignment length:660
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658
         Q5SI76_THET8     - --MIRTVALVGHAGSGKTTLTEALLYKTGAKERRGRVEEGTTTTDYTPEAKLHRTTVRTGVAPLLFRGHRVFLLDAPGYGDFVGEIRGALEAADAALVAVSAEAGVQVGTERAWTVAERLGLPRMVVVTKLDKGGDYYALLEDLRSTLGPILPIDLPLYEGGKWVGLIDVFHGKAYRYENGEEREAEVPPEERERVQRFRQEVLEAIVETDEGLLEKYLEGEEVTGEALEKAFHEAVRRGLLYPVALASGEREIGVLPLLELILEALPSPTERFGDGPPLAKVFKVQVDPFMGQVAYLRLYRGRLKPGDSLQSEAGQVRLPHLYVPMGKDLLEVEEAEAGFVLGVPKAEGLHRGMVLWQGEKPESEEVPFARLPDPNVPVALHPKGRTDEARLGEALRKLLEEDPSLKLERQEETGELLLWGHGELHLATAKERLQDYGVEVEFSVPKVPYRETIKKVAEGQGKYKKQTGGHGQYGDVWLRLEPASEYGFEWRITGGVIPSKYQEAIEEGIKEAAKKGVLAGFPVMGFKAIVYNGSYHEVDSSDLAFQIAASLAFKKVMAEAHPVLLEPIYRLKVLAPQERVGDVLSDLQARRGRILGMEQEGALSVVHAEVPLAEVLEYYKALPGLTGGAGAYTLEFSHYAEVPPHLAQRIVQERAQEG 658
               SCOP domains --d1wdta2 A:8-274 Elongation factor G (EF-G), N-terminal (G) domain                                                                                                                                                                                                          d1wdta1 A:275-377 Elongation factor G (EF-G), domain II                                                d1wdta5 A:378-454 Elongation factor G (EF-G)                                 d1wdta3 A:455-569 Elongation factor G (EF-G), domain IV                                                            d1wdta4 A:570-665 Elongation factor G (EF-G)                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1wdtA03 A:378-453 Elongation Factor G (Translational Gtpase), domain 3      -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee.....hhhhhhhhhhhhh..................hhhhhhh......eeeeeee..eeeeeee...hhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhh...eeeeeehhhhh.hhhhhhhhhhhhhh.eee.eeeeee..eeeeeee....eeeeee..eeeee..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhh.hhhhhhh....eeeeeeeeee...eeeeeeeeee.ee...eeeee....eee..eeeee..eeeee..ee...eeee..........eee.....hhhhh.........eeeeeee.hhhhhhhhhhhhhhhhhhh...eeee......eeeee.hhhhhhhhhhhhhhh...eeee......eeee...eeeeeeeee......eeeeeeeeeee....eeee.......hhhhhhhhhhhhhhhhh...........eeeeeeeee......hhhhhhhhhhhhhhhhhh...eeeeeeeeeeeeee......hhhhhhhhhh....eeee....eeee..ee.hhh.hhhhhhhhh........eeeeeeee.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1wdt A   6 GAMIRTVALVGHAGSGKTTLTEALLYKTGAKERRGRVEEGTTTTDYTPEAKLHRTTVRTGVAPLLFRGHRVFLLDAPGYGDFVGEIRGALEAADAALVAVSAEAGVQVGTERAWTVAERLGLPRMVVVTKLDKGGDYYALLEDLRSTLGPILPIDLPLYEGGKWVGLIDVFHGKAYRYENGEEREAEVPPEERERVQRFRQEVLEAIVETDEGLLEKYLEGEEVTGEALEKAFHEAVRRGLLYPVALASGEREIGVLPLLELILEALPSPTERFGDGPPLAKVFKVQVDPFMGQVAYLRLYRGRLKPGDSLQSEAGQVRLPHLYVPMGKDLLEVEEAEAGFVLGVPKAEGLHRGMVLWQGEKPESEEVPFARLPDPNVPVALHPKGRTDEARLGEALRKLLEEDPSLKLERQEETGELLLWGHGELHLATAKERLQDYGVEVEFSVPKVPYRETIKKVAEGQGKYKKQTGGHGQYGDVWLRLEPASEYGFEWRITGGVIPSKYQEAIEEGIKEAAKKGVLAGFPVMGFKAIVYNGSYHEVDSSDLAFQIAASLAFKKVMAEAHPVLLEPIYRLKVLAPQERVGDVLSDLQARRGRILGMEQEGALSVVHAEVPLAEVLEYYKALPGLTGGAGAYTLEFSHYAEVPPHLAQRIVQERAQEG 665
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: Elongation Factor G (Translational Gtpase), domain 3 (20)

Thermus thermophilus. Organism_taxid: 274. (6)

1wdtA03

A:378-453

(no "Pfam Domain" information available for 1WDT)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q5SI76_THET8 | Q5SI76)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0003924	GTPase activity	Catalysis of the reaction: GTP + H2O = GDP + phosphate.
	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.
	GO:0003746	translation elongation factor activity	Functions in chain elongation during polypeptide synthesis at the ribosome.
biological process
	GO:0006414	translational elongation	The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.

Asymmetric/Biological Unit
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Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (0, 0)

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