1XNK - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   BETA-1,4-XYLANASE FROM CHAETOMIUM THERMOPHILUM COMPLEXED WITH METHYL THIOXYLOPENTOSIDE

Authors :   J. Hakanpaa, N. Hakulinen, J. Rouvinen

Date :   05 Oct 04 (Deposition) - 10 May 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.55

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

Keywords :   Xylanase, Glycoside Hydrolase, Family 11, Glycosidase, Thioinhibitor, Sulphur Containing Inhibitor, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Janis, J. Hakanpaa, N. Hakulinen, F. M. Ibatullin, A. Hoxha, P. J. Derrick, J. Rouvinen, P. Vainiotalo
Determination Of Thioxylo-Oligosaccharide Binding To Family 11 Xylanases Using Electrospray Ionization Fourier Transfor Ion Cyclotron Resonance Mass Spectrometry And X-Ray Crystallography
Febs J. V. 272 2317 2005
PubMed-ID: 15853815 | Reference-DOI: 10.1111/J.1742-4658.2005.04659.X

Molecule 1 - ENDOXYLANASE 11A
	Chains	:	A, B
	EC Number	:	3.2.1.8
	Engineered	:	YES
	Expression System	:	HYPOCREA JECORINA
	Expression System Taxid	:	51453
	Fragment	:	CATALYTIC DOMAIN
	Organism Scientific	:	CHAETOMIUM THERMOPHILUM
	Organism Taxid	:	209285

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 7)

No.	Name	Count	Type	Full Name
1	PCA	2	Mod. Amino Acid	PYROGLUTAMIC ACID
2	SO4	3	Ligand/Ion	SULFATE ION
3	XS2	2	Ligand/Ion	METHYL4,4II,4III,4IV-TETRATHIO-BETA-D-XYLOPENTOSIDE

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID
2	SO4	1	Ligand/Ion	SULFATE ION
3	XS2	1	Ligand/Ion	METHYL4,4II,4III,4IV-TETRATHIO-BETA-D-XYLOPENTOSIDE

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID
2	SO4	2	Ligand/Ion	SULFATE ION
3	XS2	1	Ligand/Ion	METHYL4,4II,4III,4IV-TETRATHIO-BETA-D-XYLOPENTOSIDE

Biological Unit 3 (3, 14)

No.	Name	Count	Type	Full Name
1	PCA	4	Mod. Amino Acid	PYROGLUTAMIC ACID
2	SO4	6	Ligand/Ion	SULFATE ION
3	XS2	4	Ligand/Ion	METHYL4,4II,4III,4IV-TETRATHIO-BETA-D-XYLOPENTOSIDE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG B:27 , ASN B:29 , THR B:39 , HOH B:1184	BINDING SITE FOR RESIDUE SO4 B 1000
2	AC2	SOFTWARE	ARG A:27 , ASN A:29 , THR A:39 , HOH A:1256	BINDING SITE FOR RESIDUE SO4 A 1001
3	AC3	SOFTWARE	ARG B:68	BINDING SITE FOR RESIDUE SO4 B 1002
4	AC4	SOFTWARE	TRP A:19 , ASN A:45 , VAL A:47 , TYR A:78 , GLU A:87 , ARG A:123 , PRO A:127 , SER A:128 , ILE A:129 , TYR A:172 , GLU A:178 , HOH A:1002 , HOH A:1095 , HOH A:1202 , HOH A:1250 , HOH A:1251 , HOH A:1252 , HOH A:1257 , GLN B:23 , ARG B:105	BINDING SITE FOR RESIDUE XS2 A 601
5	AC5	SOFTWARE	GLN A:23 , ASN A:43 , HOH A:1090 , HOH A:1211 , TRP B:19 , ASN B:45 , VAL B:47 , TYR B:78 , PRO B:127 , SER B:128 , ILE B:129 , TYR B:172 , GLU B:178 , HOH B:1004 , HOH B:1080 , HOH B:1148 , HOH B:1189 , HOH B:1191	BINDING SITE FOR RESIDUE XS2 B 501

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

Asymmetric Unit

No.	Residues
1	Asn A:53	-	Pro A:54
2	Asn A:83	-	Pro A:84
3	Asn B:53	-	Pro B:54
4	Asn B:83	-	Pro B:84

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

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

(no "Exon" information available for 1XNK)

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:191
 aligned with Q8J1V6_9PEZI | Q8J1V6 from UniProtKB/TrEMBL  Length:261

    Alignment length:191
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216 
         Q8J1V6_9PEZI    27 QTLTSSATGTHNGYYYSFWTDGQGNIRFNLESGGQYSVTWSGNGNWVGGKGWNPGTDNRVINYTADYRPNGNSYLAVYGWTRNPLIEYYVVESFGTYDPSTGATRMGSVTTDGGTYNIYRTQRVNAPSIEGTKTFYQYWSVRTSKRTGGTVTMANHFNAWRQAGLQLGSHDYQIVATEGYYSSGSATVNVG 217
               SCOP domains d1xnka_ A: automated matches                                                                                                                                                                    SCOP domains
               CATH domains -1xnkA00 A:2-191  [code=2.60.120.180, no name defined]                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee..eeeeeee....eeeeee....eeeeeee...eeeeeeee.......eeeeeeeeeeeeeeeeeeeeeee...eeeeeeeee.........eeeeeeee..eeeeeeeeeeeee......eeeeeeeeee.....eeeeehhhhhhhhhhh.....eeeeeeeeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xnk A   1 xTLTSSATGTHNGYYYSFWTDGQGNIRFNLESGGQYSVTWSGNGNWVGGKGWNPGTDNRVINYTADYRPNGNSYLAVYGWTRNPLIEYYVVESFGTYDPSTGATRMGSVTTDGGTYNIYRTQRVNAPSIEGTKTFYQYWSVRTSKRTGGTVTMANHFNAWRQAGLQLGSHDYQIVATEGYYSSGSATVNVG 191
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190 
                            |                                                                                                                                                                                              
                            1-PCA

Chain B from PDB  Type:PROTEIN  Length:191
 aligned with Q8J1V6_9PEZI | Q8J1V6 from UniProtKB/TrEMBL  Length:261

    Alignment length:191
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216 
         Q8J1V6_9PEZI    27 QTLTSSATGTHNGYYYSFWTDGQGNIRFNLESGGQYSVTWSGNGNWVGGKGWNPGTDNRVINYTADYRPNGNSYLAVYGWTRNPLIEYYVVESFGTYDPSTGATRMGSVTTDGGTYNIYRTQRVNAPSIEGTKTFYQYWSVRTSKRTGGTVTMANHFNAWRQAGLQLGSHDYQIVATEGYYSSGSATVNVG 217
               SCOP domains d1xnkb_ B: automated matches                                                                                                                                                                    SCOP domains
               CATH domains -1xnkB00 B:2-191  [code=2.60.120.180, no name defined]                                                                                                                                          CATH domains
           Pfam domains (1) --------Glyco_hydro_11-1xnkB01 B:9-190                                                                                                                                                        - Pfam domains (1)
           Pfam domains (2) --------Glyco_hydro_11-1xnkB02 B:9-190                                                                                                                                                        - Pfam domains (2)
         Sec.struct. author ......eeeee..eeeeeee....eeeeee....eeeeeee...eeeeeeee.......eeeeeeeeeeeeeeeeeeeeeee...eeeeeeeee.........eeeeeeee..eeeeeeeeeeeee......eeeeeeeeee.....eeeeehhhhhhhhhhh.....eeeeeeeeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xnk B   1 xTLTSSATGTHNGYYYSFWTDGQGNIRFNLESGGQYSVTWSGNGNWVGGKGWNPGTDNRVINYTADYRPNGNSYLAVYGWTRNPLIEYYVVESFGTYDPSTGATRMGSVTTDGGTYNIYRTQRVNAPSIEGTKTFYQYWSVRTSKRTGGTVTMANHFNAWRQAGLQLGSHDYQIVATEGYYSSGSATVNVG 191
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190 
                            1-PCA

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Concanavalin A-like lectins/glucanases (797)

Superfamily: Concanavalin A-like lectins/glucanases (797)

Family: Xylanase/endoglucanase 11/12 (93)

Protein domain: automated matches (10)

Chaetomium thermophilum [TaxId: 209285] (1)

1a	d1xnka_	A:
1b	d1xnkb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: [code=2.60.120.180, no name defined] (77)

Chaetomium thermophilum. Organism_taxid: 209285. (2)

1a	1xnkA00	A:2-191
1b	1xnkB00	B:2-191

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Concanavalin (293)

Family: Glyco_hydro_11 (14)

Chaetomium thermophilum (1)

1a	Glyco_hydro_11-1xnkB01	B:9-190
1b	Glyco_hydro_11-1xnkB02	B:9-190

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q8J1V6_9PEZI | Q8J1V6)

molecular function
	GO:0031176	endo-1,4-beta-xylanase activity	Catalysis of the endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0016798	hydrolase activity, acting on glycosyl bonds	Catalysis of the hydrolysis of any glycosyl bond.
	GO:0004553	hydrolase activity, hydrolyzing O-glycosyl compounds	Catalysis of the hydrolysis of any O-glycosyl bond.
biological process
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0000272	polysaccharide catabolic process	The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
	GO:0045493	xylan catabolic process	The chemical reactions and pathways resulting in the breakdown of xylan, a polymer containing a beta-1,4-linked D-xylose backbone.

Asymmetric Unit
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	Cis Peptide Bonds
		Asn A:53 - Pro A:54	[ RasMol ]
		Asn A:83 - Pro A:84	[ RasMol ]
		Asn B:53 - Pro B:54	[ RasMol ]
		Asn B:83 - Pro B:84	[ RasMol ]

Biological Units
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	1xnk
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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