2XQX - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF THE FAMILY 32 CARBOHYDRATE-BINDING MODULE FROM STREPTOCOCCUS PNEUMONIAE ENDOD

Authors :   D. W. Abbott, A. B. Boraston

Date :   07 Sep 10 (Deposition) - 03 Nov 10 (Release) - 11 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.01

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

Keywords :   Sugar Binding Protein, Carbohydrate Binding, Beta-Sandwhich (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. W. Abbott, A. B. Boraston
Structural Analysis Of A Putative Family 32 Carbohydrate-Binding Module From The Streptococcus Pneumoniae Enzyme Endod.
Acta Crystallogr. , Sect. F V. 67 429 2011
PubMed-ID: 21505233 | Reference-DOI: 10.1107/S1744309111001874

Molecule 1 - ENDO-BETA-N-ACETYLGLUCOSAMINIDASE D
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET28
	Fragment	:	CBM32, RESIDUES 804-948
	Organism Scientific	:	STREPTOCOCCUS PNEUMONIAE
	Organism Taxid	:	170187
	Strain	:	TIGR4
	Synonym	:	ENDOD

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 14)

No.	Name	Count	Type	Full Name
1	ACT	4	Ligand/Ion	ACETATE ION
2	CA	2	Ligand/Ion	CALCIUM ION
3	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	CA	-1	Ligand/Ion	CALCIUM ION
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	CA	-1	Ligand/Ion	CALCIUM ION
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:827 , ASN A:830 , THR A:832 , ASP A:838 , TYR A:941 , ASN A:942	BINDING SITE FOR RESIDUE CA A1949
2	AC2	SOFTWARE	GLY B:827 , ASN B:830 , THR B:832 , ASP B:838 , TYR B:941 , ASN B:942	BINDING SITE FOR RESIDUE CA B1949
3	AC3	SOFTWARE	ARG A:902 , ALA B:843 , GLN B:844	BINDING SITE FOR RESIDUE ACT B1950
4	AC4	SOFTWARE	GLY A:868 , VAL A:874 , GLY B:903	BINDING SITE FOR RESIDUE ACT A1950
5	AC5	SOFTWARE	GLY A:903 , GLY B:868 , GLY B:871 , VAL B:874 , HOH B:2133	BINDING SITE FOR RESIDUE ACT B1951
6	AC6	SOFTWARE	HOH A:2096 , HOH A:2122	BINDING SITE FOR RESIDUE ACT A1951

(no "SS Bond" information available for 2XQX)

Asymmetric Unit

No.	Residues
1	Glu A:820	-	Gly A:821

(no "SAP(SNP)/Variant" information available for 2XQX)

(no "PROSITE Motif" information available for 2XQX)

(no "Exon" information available for 2XQX)

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:147
 aligned with A0A0H2UNT5_S | A0A0H2UNT5 from UniProtKB/TrEMBL  Length:1659

    Alignment length:147
                                   824       834       844       854       864       874       884       894       904       914       924       934       944       954       
         A0A0H2UNT5_S   815 AENIVPGATVIDSTFPKTEGGEGIEGMLNGTITSLSDKWSSAQLSGSVDIRLTKPRTVVRWVMDHAGAGGESVNDGLMNTKDFDLYYKDADGEWKLAKEVRGNKAHVTDITLDKPITAQDWRLNVVTSDNGTPWKAIRIYNWKMYEK 961
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee.........hhhhhh..........eee....eeeeeeeeeeeeeeeeeeee.hhhh...........eeeeeee.....eeeeeee......eeeeeeeeeeeeeeeeeeeee.........eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xqx A 802 ASNIVPGATVIDSTFPKTEGGEGIEGmLNGTITSLSDKWSSAQLSGSVDIRLTKPRTVVRWVmDHAGAGGESVNDGLmNTKDFDLYYKDADGEWKLAKEVRGNKAHVTDITLDKPITAQDWRLNVVTSDNGTPWKAIRIYNWKmYEK 948
                                   811       821      |831       841       851       861  |    871       881       891       901       911       921       931       941   |   
                                                    828-MSE                             864-MSE        879-MSE                                                           945-MSE

Chain A from PDB  Type:PROTEIN  Length:147
 aligned with Q93HW0_STREE | Q93HW0 from UniProtKB/TrEMBL  Length:1646

    Alignment length:147
                                   811       821       831       841       851       861       871       881       891       901       911       921       931       941       
         Q93HW0_STREE   802 AENIVPGATVIDSTFPKTEGGEGIEGMLNGTITSLSDKWSSAQLSGSVDIRLTKPRTVVRWVMDHAGAGGESVNDGLMNTKDFDLYYKDADGEWKLAKEVRGNKAHVTDITLDKPITAQDWRLNVVTSDNGTPWKAIRIYNWKMYEK 948
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee.........hhhhhh..........eee....eeeeeeeeeeeeeeeeeeee.hhhh...........eeeeeee.....eeeeeee......eeeeeeeeeeeeeeeeeeeee.........eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xqx A 802 ASNIVPGATVIDSTFPKTEGGEGIEGmLNGTITSLSDKWSSAQLSGSVDIRLTKPRTVVRWVmDHAGAGGESVNDGLmNTKDFDLYYKDADGEWKLAKEVRGNKAHVTDITLDKPITAQDWRLNVVTSDNGTPWKAIRIYNWKmYEK 948
                                   811       821      |831       841       851       861  |    871       881       891       901       911       921       931       941   |   
                                                    828-MSE                             864-MSE        879-MSE                                                           945-MSE

Chain B from PDB  Type:PROTEIN  Length:146
 aligned with A0A0H2UNT5_S | A0A0H2UNT5 from UniProtKB/TrEMBL  Length:1659

    Alignment length:146
                                   825       835       845       855       865       875       885       895       905       915       925       935       945       955      
         A0A0H2UNT5_S   816 ENIVPGATVIDSTFPKTEGGEGIEGMLNGTITSLSDKWSSAQLSGSVDIRLTKPRTVVRWVMDHAGAGGESVNDGLMNTKDFDLYYKDADGEWKLAKEVRGNKAHVTDITLDKPITAQDWRLNVVTSDNGTPWKAIRIYNWKMYEK 961
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee.........hhhhhh..........eee....eeeeeeeeeeeeeeeeeee.hhhhh...........eeeeeee.....eeeeeee......eeeeeeeeeeeeeeeeeeeee.........eee.eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xqx B 803 SNIVPGATVIDSTFPKTEGGEGIEGmLNGTITSLSDKWSSAQLSGSVDIRLTKPRTVVRWVmDHAGAGGESVNDGLmNTKDFDLYYKDADGEWKLAKEVRGNKAHVTDITLDKPITAQDWRLNVVTSDNGTPWKAIRIYNWKmYEK 948
                                   812       822     | 832       842       852       862 |     872      |882       892       902       912       922       932       942  |   
                                                   828-MSE                             864-MSE        879-MSE                                                           945-MSE

Chain B from PDB  Type:PROTEIN  Length:146
 aligned with Q93HW0_STREE | Q93HW0 from UniProtKB/TrEMBL  Length:1646

    Alignment length:146
                                   812       822       832       842       852       862       872       882       892       902       912       922       932       942      
         Q93HW0_STREE   803 ENIVPGATVIDSTFPKTEGGEGIEGMLNGTITSLSDKWSSAQLSGSVDIRLTKPRTVVRWVMDHAGAGGESVNDGLMNTKDFDLYYKDADGEWKLAKEVRGNKAHVTDITLDKPITAQDWRLNVVTSDNGTPWKAIRIYNWKMYEK 948
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee.........hhhhhh..........eee....eeeeeeeeeeeeeeeeeee.hhhhh...........eeeeeee.....eeeeeee......eeeeeeeeeeeeeeeeeeeee.........eee.eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xqx B 803 SNIVPGATVIDSTFPKTEGGEGIEGmLNGTITSLSDKWSSAQLSGSVDIRLTKPRTVVRWVmDHAGAGGESVNDGLmNTKDFDLYYKDADGEWKLAKEVRGNKAHVTDITLDKPITAQDWRLNVVTSDNGTPWKAIRIYNWKmYEK 948
                                   812       822     | 832       842       852       862 |     872      |882       892       902       912       922       932       942  |   
                                                   828-MSE                             864-MSE        879-MSE                                                           945-MSE

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 '\|'

(no "SCOP Domain" information available for 2XQX)

(no "CATH Domain" information available for 2XQX)

(no "Pfam Domain" information available for 2XQX)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q93HW0_STREE | Q93HW0)

molecular function
	GO:0033925	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity	Catalysis of the endohydrolysis of the N,N'-diacetylchitobiosyl unit in high-mannose glycopeptides and glycoproteins containing the -[Man(GlcNAc)2]Asn-structure. One N-acetyl-D-glucosamine residue remains attached to the protein; the rest of the oligosaccharide is released intact.
cellular component
	GO:0005618	cell wall	The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain A,B (A0A0H2UNT5_S | A0A0H2UNT5)

Asymmetric Unit
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		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Glu A:820 - Gly A:821	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	Q93HW0_STREE \| Q93HW0
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UniProtKB/TrEMBL
	A0A0H2UNT5_S \| A0A0H2UNT5	:	2l7y
	Q93HW0_STREE \| Q93HW0	:	2w91 2w92

2w91	STRUCTURE OF A STREPTOCOCCUS PNEUMONIAE FAMILY 85 GLYCOSIDE HYDROLASE, ENDO-D.
2w92	STRUCTURE OF A STREPTOCOCCUS PNEUMONIAE FAMILY 85 GLYCOSIDE HYDROLASE, ENDO-D, IN COMPLEX WITH NAG-THIAZOLINE.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 14)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

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Related Entries Specified in the PDB File