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Biological Unit 2 (Jmol Viewer)

Title :   YCHF PROTEIN (HI0393)

Authors :   A. Teplyakov, G. L. Gilliland, Structure 2 Function Project (S2F)

Date :   30 May 01 (Deposition) - 25 Mar 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Nucleotide-Binding Fold, Structural Genomics, Structure 2 Function Project, S2F, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Teplyakov, G. L. Gilliland
Crystal Structure Of The Ychf Protein Reveals Binding Sites For Gtp And Nucleic Acid
J. Bacteriol. V. 185 4031 2003
PubMed-ID: 12837776 | Reference-DOI: 10.1128/JB.185.14.4031-4037.2003
(for further references see the PDB file header)

Molecule 1 - YCHF PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	YCHF
	Organism Scientific	:	HAEMOPHILUS INFLUENZAE
	Organism Taxid	:	727
	Synonym	:	HI0393, PROBABLE GTP-BINDING PROTEIN HI0393

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1JAL)

(no "Site" information available for 1JAL)

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

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_OBG	PS51710	OBG-type guanine nucleotide-binding (G) domain profile.	YCHF_HAEIN	3-256	2	A:3-256 B:3-256

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_OBG	PS51710	OBG-type guanine nucleotide-binding (G) domain profile.	YCHF_HAEIN	3-256	1	A:3-256 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_OBG	PS51710	OBG-type guanine nucleotide-binding (G) domain profile.	YCHF_HAEIN	3-256	1	- B:3-256

(no "Exon" information available for 1JAL)

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:348
 aligned with YCHF_HAEIN | P44681 from UniProtKB/Swiss-Prot  Length:363

    Alignment length:363
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360   
           YCHF_HAEIN     1 MGFKCGIVGLPNVGKSTLFNALTKAGIEAANYPFCTIEPNTGVVPMPDPRLDALAEIVKPERILPTTMEFVDIAGLVAGASKGEGLGNKFLANIRETDAIGHVVRCFENDDIVHVAGKIDPLDDIDTINTELALADLDSCERAIQRLQKRAKGGDKEAKFELSVMEKILPVLENAGMIRSVGLDKEELQAIKSYNFLTLKPTMYIANVNEDGFENNPYLDRVREIAAKEGAVVVPVCAAIESEIAELDDEEKVEFLQDLGIEEPGLNRVIRAGYALLNLQTYFTAGVKEVRAWTVSVGATAPKAAAVIHTDFEKGFIRAEVIAYEDFIQFNGENGAKEAGKWRLEGKDYIVQDGDVMHFRFNV 363
               SCOP domains d1jala1 A:1-278 YchF GTP-b      inding protein N-terminal domain                                                                                                                                                                                                                      d1jala2 A:279-363 YchF GTP-binding protein, C-terminal domain                         SCOP domains
               CATH domains 1jalA01 A:1-47,A:66-119,A:      201-278        1jalA02           1jalA01 A:1-47,A:66-119,A:201-278                     1jalA03 A:120-200 TGS-like domain                                                1jalA01 A:1-47,A:66-119,A:201-278                                             1jalA02 A:48-65,A:279-363  [code=3.10.20.30, no name defined]                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhh.------..........eee..hhhhhhhhhhhh..eee..eeeeee......hhhhhhhhh.hhhhhhhh..eeeeeee....---------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhh......eeeeee........hhhhhhhhhhhhhh..eeeeehhhhhhhhhhh....hhhhhh........hhhhhhhhhhhh.eeeeeee...eeeeeeee...hhhhhhhhhhhhhhhhh.eeeeehhhhhhhh.hhhhhhhh...eee..........eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --G_OBG  PDB: A:3-256 UniProt: 3-256                                                                                                                                                                                                                            ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jal A   1 MGFKCGIVGLPNVGKSTLFNALTKAG------PFCTIEPNTGVVPMPDPRLDALAEIVKPERILPTTMEFVDIAGLVAGASKGEGLGNKFLANIRETDAIGHVVRCFEN---------IDPLDDIDTINTELALADLDSCERAIQRLQKRAKGGDKEAKFELSVMEKILPVLENAGMIRSVGLDKEELQAIKSYNFLTLKPTMYIANVNEDGFENNPYLDRVREIAAKEGAVVVPVCAAIESEIAELDDEEKVEFLQDLGIEEPGLNRVIRAGYALLNLQTYFTAGVKEVRAWTVSVGATAPKAAAVIHTDFEKGFIRAEVIAYEDFIQFNGENGAKEAGKWRLEGKDYIVQDGDVMHFRFNV 363
                                    10        20     |   -  |     40        50        60        70        80        90       100        |-       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360   
                                                    26     33                                                                         109       119

Chain B from PDB  Type:PROTEIN  Length:335
 aligned with YCHF_HAEIN | P44681 from UniProtKB/Swiss-Prot  Length:363

    Alignment length:363
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360   
           YCHF_HAEIN     1 MGFKCGIVGLPNVGKSTLFNALTKAGIEAANYPFCTIEPNTGVVPMPDPRLDALAEIVKPERILPTTMEFVDIAGLVAGASKGEGLGNKFLANIRETDAIGHVVRCFENDDIVHVAGKIDPLDDIDTINTELALADLDSCERAIQRLQKRAKGGDKEAKFELSVMEKILPVLENAGMIRSVGLDKEELQAIKSYNFLTLKPTMYIANVNEDGFENNPYLDRVREIAAKEGAVVVPVCAAIESEIAELDDEEKVEFLQDLGIEEPGLNRVIRAGYALLNLQTYFTAGVKEVRAWTVSVGATAPKAAAVIHTDFEKGFIRAEVIAYEDFIQFNGENGAKEAGKWRLEGKDYIVQDGDVMHFRFNV 363
               SCOP domains d1jalb1 B:1-278 YchF GTP-               binding protein N-terminal domain                                                                                                                                                                                                             d1jalb2 B:279-363 YchF GTP-binding protein, C-terminal domain                         SCOP domains
               CATH domains 1jalB01 B:1-47,B:66-108,B               :201-271jalB02           1jalB01 B:1-47,B:66-108,B:201-278                       1jalB03 B:122-200 TGS-like domain                                              1jalB01 B:1-47,B:66-108,B:201-278                                             1jalB02 B:48-65,B:279-363  [code=3.10.20.30, no name defined]                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhh---------------..eee...hhhhhhhhhhh..eee..eeeeee................hhhhhhhhh.eeeeeee...-------------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhh.eeeeee........hhhhhhhhhhhhhhh.eeeeehhhhhhhhhh..hhhhhhhhhh......hhhhhhhhhhhhh.eeeeee....eeeeeeee...hhhhhhhhhhhhhhhhh.eeeeehhhhhhhh..hhhhhhh...eee..........eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --G_OBG  PDB: B:3-256 UniProt: 3-256                                                                                                                                                                                                                            ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jal B   1 MGFKCGIVGLPNVGKSTLFNALTKA---------------TGVVPMPDPRLDALAEIVKPERILPTTMEFVDIAGLVAGASKGEGLGNKFLANIRETDAIGHVVRCFE-------------LDDIDTINTELALADLDSCERAIQRLQKRAKGGDKEAKFELSVMEKILPVLENAGMIRSVGLDKEELQAIKSYNFLTLKPTMYIANVNEDGFENNPYLDRVREIAAKEGAVVVPVCAAIESEIAELDDEEKVEFLQDLGIEEPGLNRVIRAGYALLNLQTYFTAGVKEVRAWTVSVGATAPKAAAVIHTDFEKGFIRAEVIAYEDFIQFNGENGAKEAGKWRLEGKDYIVQDGDVMHFRFNV 363
                                    10        20    |    -         -|       50        60        70        80        90       100       | -         - |     130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360   
                                                   25              41                                                                108           122

Legend:		→ Mismatch	(orange background)
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		→ 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 Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Haemophilus influenzae. Organism_taxid: 727. (5)

1a	1jalA01	A:1-47,A:66-119,A:201-278
1b	1jalB01	B:1-47,B:66-108,B:201-278

Architecture: Roll (3276)

Topology: Ubiquitin-like (UB roll) (674)

Homologous Superfamily: [code=3.10.20.30, no name defined] (153)

Haemophilus influenzae. Organism_taxid: 727. (1)

2a	1jalA02	A:48-65,A:279-363
2b	1jalB02	B:48-65,B:279-363

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: DNA polymerase; domain 1 (617)

Homologous Superfamily: TGS-like domain (3)

Haemophilus influenzae. Organism_taxid: 727. (1)

3a	1jalA03	A:120-200
3b	1jalB03	B:122-200

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (YCHF_HAEIN | P44681)


GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0016887	ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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:0043023	ribosomal large subunit binding	Interacting selectively and non-covalently with any part of the larger ribosomal subunit.
GO:0043022	ribosome binding	Interacting selectively and non-covalently with any part of a ribosome.

Asymmetric Unit
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