3VU1 - JenaLib

Title :   CRYSTAL STRUCTURE OF THE C-TERMINAL GLOBULAR DOMAIN OF OLIGOSACCHARYLTRANSFERASE (PHAGLB-L, O74088_PYRHO) FROM PYROCOCCUS HORIKOSHII

Authors :   J. Nyirenda, S. Matsumoto, T. Saitoh, N. Maita, N. N. Noda, F. Inagaki, D

Date :   13 Jun 12 (Deposition) - 23 Jan 13 (Release) - 23 Jan 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)

Keywords :   Glycotransferase, Asn-Glycosylation, Membrane, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Nyirenda, S. Matsumoto, T. Saitoh, N. Maita, N. N. Noda, F. Inagaki, D. Kohda
Crystallographic And Nmr Evidence For Flexibility In Oligosaccharyltransferases And Its Catalytic Significance
Structure V. 21 32 2013
PubMed-ID: 23177926 | Reference-DOI: 10.1016/J.STR.2012.10.011

Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN PH0242
	Chains	:	A, B
	EC Number	:	2.4.1.119
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-41B(+)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL GLOBULAR DOMAIN
	Gene	:	AGLB
	Organism Scientific	:	PYROCOCCUS HORIKOSHII
	Organism Taxid	:	70601
	Strain	:	OT3
	Synonym	:	OLIGOSACCHARYLTRANSFERASE AGLB

Structural Features

Chains, Units

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 4)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	CL	2	Ligand/Ion	CHLORIDE ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:556 , ALA A:765 , HIS A:799 , GLU A:802	BINDING SITE FOR RESIDUE CA A 1001
2	AC2	SOFTWARE	ARG A:768 , ARG A:872	BINDING SITE FOR RESIDUE CL A 1002
3	AC3	SOFTWARE	GLU B:556 , ALA B:765 , HIS B:799 , GLU B:802	BINDING SITE FOR RESIDUE CA B 1001
4	AC4	SOFTWARE	ARG B:768 , ARG B:872	BINDING SITE FOR RESIDUE CL B 1002

SS Bonds (2, 2)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:488
 aligned with O74088_PYRHO | O74088 from UniProtKB/TrEMBL  Length:976

    Alignment length:496
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   976      
                                   496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886       896       906       916       926       936       946       956       966       976      
         O74088_PYRHO   487 EIEVTGWEQALKWLRSNTSKYATATSWWDYGYWIESSLLGNRRASADGGHARDRDHILALFLARDGNISEVDFESWELNYFIIYLNDWAKFNAISYLGGAITRKEYNGDENGRGRVTTILLTQAAGNVYVNPYARIVIKVIQQNKTRRIAVNIGQLECSPILSVAFPGNIKIKGSGRCSDGSPFPYVVYLTPSLGVLAYYKVATSNFVKLAFGIPTSSYSEFAEKLFSNFIPVYQYGSVIVYEFRPFAIYKIEDFINGTWREVGKLSPGKHTLRLYISAFGRDIKNATLYVYALNGTKIIKRIKVGEIKYMNHLEEYPIIVNVTLPTAQKYRFILAQKGPVGVLTGPVRVNGKITNPAYIMREGESGRLELKVGVDKEYTADLYLRATFIYLVRKGGKSNEDYDASFEPHMDTFFITKLKEGIKLRPGENEIVVNAEMPKNAISSYKEKLEKEHGDKLIIRGIRVEPVFIVEKEYTMIEVSASAPHHSSE------   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh.....eee.................--------.hhhhhhhhhhhh.hhhhh.hhhhhh..eeeee.hhhhhhhhhhhhh...hhhhhhh..........eeeeee...eeee....eeeeeee....eeeeeee..eeee..eeee....eeee...ee.......eeeee...eeeeee.hhh.hhhhhhhhh.......hhhhhhhhheeeeeee..eeeeee..eeeeeeeeee..eeee......eeeeeeeeeee....eeeeeeeeeeee..eeeeeeeeeeeeee.......eeeeeee....eeeeeeeeeeee.ee...eee..eee..........eeeeeeeeee...eeeeeeeeeeeeeeeee..........eeeeeeeeeeeeeeeeeeee..eeeeeeeeee...hhhhhhhhhhhhhhh..eeeeeeeeeeeeeeeeeeeeeeee............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vu1 A 487 EIEVTGWEQALKWLRSNTSKYATATSWWDYGYWIESSLLGNRR--------RDRDHILALFLARDGNISEVDFESWELNYFIIYLNDWAKFNAISYLGGAITRKEYNGDENGRGRVTTILLTQAAGNVYVNPYARIVIKVIQQNKTRRIAVNIGQLECSPILSVAFPGNIKIKGSGRCSDGSPFPYVVYLTPSLGVLAYYKVATSNFVKLAFGIPTSSYSEFAEKLFSNFIPVYQYGSVIVYEFRPFAIYKIEDFINGTWREVGKLSPGKHTLRLYISAFGRDIKNATLYVYALNGTKIIKRIKVGEIKYMNHLEEYPIIVNVTLPTAQKYRFILAQKGPVGVLTGPVRVNGKITNPAYIMREGESGRLELKVGVDKEYTADLYLRATFIYLVRKGGKSNEDYDASFEPHMDTFFITKLKEGIKLRPGENEIVVNAEMPKNAISSYKEKLEKEHGDKLIIRGIRVEPVFIVEKEYTMIEVSASAPHHHHHHHHHHH 986
                                   496       506       516       526  |      - |     546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886       896       906       916       926       936       946       956       966      |980      
                                                                    529      538                                                                                                                                                                                                                                                                                                                                                                                                                                                973|        
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 978

Chain B from PDB  Type:PROTEIN  Length:490
 aligned with O74088_PYRHO | O74088 from UniProtKB/TrEMBL  Length:976

    Alignment length:490
                                   495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945       955       965       975
         O74088_PYRHO   486 TEIEVTGWEQALKWLRSNTSKYATATSWWDYGYWIESSLLGNRRASADGGHARDRDHILALFLARDGNISEVDFESWELNYFIIYLNDWAKFNAISYLGGAITRKEYNGDENGRGRVTTILLTQAAGNVYVNPYARIVIKVIQQNKTRRIAVNIGQLECSPILSVAFPGNIKIKGSGRCSDGSPFPYVVYLTPSLGVLAYYKVATSNFVKLAFGIPTSSYSEFAEKLFSNFIPVYQYGSVIVYEFRPFAIYKIEDFINGTWREVGKLSPGKHTLRLYISAFGRDIKNATLYVYALNGTKIIKRIKVGEIKYMNHLEEYPIIVNVTLPTAQKYRFILAQKGPVGVLTGPVRVNGKITNPAYIMREGESGRLELKVGVDKEYTADLYLRATFIYLVRKGGKSNEDYDASFEPHMDTFFITKLKEGIKLRPGENEIVVNAEMPKNAISSYKEKLEKEHGDKLIIRGIRVEPVFIVEKEYTMIEVSASAPHHSS 975
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhh.....eee.........................hhhhhhhhhhhhh.hhhhh.hhhhhh..eeeee.hhhhhhhhhhhhh...hhhhhhh..........eeeeeee..eeee....eeeeeee....eeeeeee..eeee..eeee....eeee...ee.......eeeee...eeeeee.hhh.hhhhhhhhh.......hhhhhhhhheeeeeee..eeeeee..eeeeeeeeee..eeee......eeeeeeeeeee....eeeeeeeeeeee..eeeeeeeeeeeeee.......eeeeeee....eeeeeeeeeeee.eeeeeeee..eee..........eeeeeeeeee.....eeeeeeeeeeeeeee..........eeeeeeeeeeeeeeeeee....eeeeeeeeee....hhhhhhhhhhhhhh..eeeeeeeeeeeeeeeeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vu1 B 486 TEIEVTGWEQALKWLRSNTSKYATATSWWDYGYWIESSLLGNRRASADGGHARDRDHILALFLARDGNISEVDFESWELNYFIIYLNDWAKFNAISYLGGAITRKEYNGDENGRGRVTTILLTQAAGNVYVNPYARIVIKVIQQNKTRRIAVNIGQLECSPILSVAFPGNIKIKGSGRCSDGSPFPYVVYLTPSLGVLAYYKVATSNFVKLAFGIPTSSYSEFAEKLFSNFIPVYQYGSVIVYEFRPFAIYKIEDFINGTWREVGKLSPGKHTLRLYISAFGRDIKNATLYVYALNGTKIIKRIKVGEIKYMNHLEEYPIIVNVTLPTAQKYRFILAQKGPVGVLTGPVRVNGKITNPAYIMREGESGRLELKVGVDKEYTADLYLRATFIYLVRKGGKSNEDYDASFEPHMDTFFITKLKEGIKLRPGENEIVVNAEMPKNAISSYKEKLEKEHGDKLIIRGIRVEPVFIVEKEYTMIEVSASAPHHSS 975
                                   495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945       955       965       975

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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

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