2CBV - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   BETA-GLUCOSIDASE FROM THERMOTOGA MARITIMA IN COMPLEX WITH CALYSTEGINE B2

Authors :   T. M. Gloster, R. Madsen, G. J. Davies

Date :   09 Jan 06 (Deposition) - 03 Feb 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Glycoside Hydrolase, Inhibitor, Transition State Mimic, Family 1, Carbohydrate Metabolism, Cellulose Degradation, Glycosidase, Hydrolase, Polysaccharide Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. M. Gloster, R. Madsen, G. J. Davies
Dissection Of Conformationally Restricted Inhibitors Binding To A Beta-Glucosidase.
Chembiochem V. 7 738 2006
PubMed-ID: 16628756 | Reference-DOI: 10.1002/CBIC.200600005
(for further references see the PDB file header)

Molecule 1 - BETA-GLUCOSIDASE A
	Chains	:	A, B
	EC Number	:	3.2.1.21
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336
	Synonym	:	GENTIOBIASE, CELLOBIASE, BETA-D-GLUCOSIDE GLUCOHYDROLASE

		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 (2, 4)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	CGB	2	Ligand/Ion	CALYSTEGINE B2

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	CGB	1	Ligand/Ion	CALYSTEGINE B2

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	CGB	1	Ligand/Ion	CALYSTEGINE B2

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:54 , TYR A:421 , HOH A:2013 , HOH A:2419	BINDING SITE FOR RESIDUE ACT A1448
2	AC2	SOFTWARE	ASP B:278 , SER B:281 , GLU B:282 , HOH B:2269 , HOH B:2270	BINDING SITE FOR RESIDUE ACT B1446
3	AC3	SOFTWARE	GLN A:20 , HIS A:121 , TRP A:122 , ASN A:165 , GLU A:166 , TRP A:324 , GLU A:351 , TRP A:398 , GLU A:405 , TRP A:406	BINDING SITE FOR RESIDUE CGB A1447
4	AC4	SOFTWARE	GLN B:20 , HIS B:121 , TRP B:122 , ASN B:165 , GLU B:166 , TRP B:324 , GLU B:351 , TRP B:398 , GLU B:405 , TRP B:406	BINDING SITE FOR RESIDUE CGB B1445

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

Asymmetric Unit

No.	Residues
1	Ala A:181	-	Pro A:182
2	Trp A:398	-	Ser A:399
3	Ala B:181	-	Pro B:182
4	Trp B:398	-	Ser B:399

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLYCOSYL_HYDROL_F1_2	PS00653	Glycosyl hydrolases family 1 N-terminal signature.	BGLA_THEMA	10-24	2	A:10-24 B:10-24
2	GLYCOSYL_HYDROL_F1_1	PS00572	Glycosyl hydrolases family 1 active site.	BGLA_THEMA	347-355	2	A:347-355 B:347-355

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLYCOSYL_HYDROL_F1_2	PS00653	Glycosyl hydrolases family 1 N-terminal signature.	BGLA_THEMA	10-24	1	A:10-24 -
2	GLYCOSYL_HYDROL_F1_1	PS00572	Glycosyl hydrolases family 1 active site.	BGLA_THEMA	347-355	1	A:347-355 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLYCOSYL_HYDROL_F1_2	PS00653	Glycosyl hydrolases family 1 N-terminal signature.	BGLA_THEMA	10-24	1	- B:10-24
2	GLYCOSYL_HYDROL_F1_1	PS00572	Glycosyl hydrolases family 1 active site.	BGLA_THEMA	347-355	1	- B:347-355

(no "Exon" information available for 2CBV)

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:443
 aligned with BGLA_THEMA | Q08638 from UniProtKB/Swiss-Prot  Length:446

    Alignment length:444
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442    
           BGLA_THEMA     3 VKKFPEGFLWGVATASYQIEGSPLADGAGMSIWHTFSHTPGNVKNGDTGDVACDHYNRWKEDIEIIEKLGVKAYRFSISWPRILPEGTGRVNQKGLDFYNRIIDTLLEKGITPFVTIYHWDLPFALQLKGGWANREIADWFAEYSRVLFENFGDRVKNWITLNEPWVVAIVGHLYGVHAPGMRDIYVAFRAVHNLLRAHARAVKVFRETVKDGKIGIVFNNGYFEPASEKEEDIRAVRFMHQFNNYPLFLNPIYRGDYPELVLEFAREYLPENYKDDMSEIQEKIDFVGLNYYSGHLVKFDPDAPAKVSFVERDLPKTAMGWEIVPEGIYWILKKVKEEYNPPEVYITENGAAFDDVVSEDGRVHDQNRIDYLKAHIGQAWKAIQEGVPLKGYFVWSLLDNFEWAEGYSKRFGIVYVDYSTQKRIVKDSGYWYSNVVKNNGLED 446
               SCOP domains d2cbva_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 2cbvA00 A:3-446 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee.....eeeee.hhhhhh...hhhhh..hhhhhhhh....hhhhh......hhhhhhhhhhhhhhhhh..eeeee.hhhhhh.......hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeeeeee....-hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhh....eeeeeeeeeeeeee.........................hhhhhhhhhhhhhhhh...eeeeee...............hhhhhhhhhhhhhhhhhhhhh...eeeeeee......hhhhhhhh....eee......eeehhhhhhhhhhhhhhee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------GLYCOSYL_HYDROL----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLYCOSYL_------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2cbv A   3 VKKFPEGFLWGVATASYQIEGSPLADGAGMSIWHTFSHTPGNVKNGDTGDVACDHYNRWKEDIEIIEKLGVKAYRFSISWPRILPEGTGRVNQKGLDFYNRIIDTLLEKGITPFVTIYHWDLPFALQLKGGWANREIADWFAEYSRVLFENFGDRVKNWITLNEPWVVAIVGHLYGVHAPGMRDIYVAFRAVHNLLRAHARAVKVFRETVKDGKIGIVFNNGYFEPASEK-EDIRAVRFMHQFNNYPLFLNPIYRGDYPELVLEFAREYLPENYKDDMSEIQEKIDFVGLNYYSGHLVKFDPDAPAKVSFVERDLPKTAMGWEIVPEGIYWILKKVKEEYNPPEVYITENGAAFDDVVSEDGRVHDQNRIDYLKAHIGQAWKAIQEGVPLKGYFVWSLLDNFEWAEGYSKRFGIVYVDYSTQKRIVKDSGYWYSNVVKNNGLED 446
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232 |     242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442    
                                                                                                                                                                                                                                                               232 |                                                                                                                                                                                                                    
                                                                                                                                                                                                                                                                 234

Chain B from PDB  Type:PROTEIN  Length:442
 aligned with BGLA_THEMA | Q08638 from UniProtKB/Swiss-Prot  Length:446

    Alignment length:442
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442  
           BGLA_THEMA     3 VKKFPEGFLWGVATASYQIEGSPLADGAGMSIWHTFSHTPGNVKNGDTGDVACDHYNRWKEDIEIIEKLGVKAYRFSISWPRILPEGTGRVNQKGLDFYNRIIDTLLEKGITPFVTIYHWDLPFALQLKGGWANREIADWFAEYSRVLFENFGDRVKNWITLNEPWVVAIVGHLYGVHAPGMRDIYVAFRAVHNLLRAHARAVKVFRETVKDGKIGIVFNNGYFEPASEKEEDIRAVRFMHQFNNYPLFLNPIYRGDYPELVLEFAREYLPENYKDDMSEIQEKIDFVGLNYYSGHLVKFDPDAPAKVSFVERDLPKTAMGWEIVPEGIYWILKKVKEEYNPPEVYITENGAAFDDVVSEDGRVHDQNRIDYLKAHIGQAWKAIQEGVPLKGYFVWSLLDNFEWAEGYSKRFGIVYVDYSTQKRIVKDSGYWYSNVVKNNGL 444
               SCOP domains d2cbvb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2cbvB00 B:3-444 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.....eeeee.hhhhhh...hhhhh..hhhhhhhh....hhhhh......hhhhhhhhhhhhhhhh...eeeee.hhhhhh.......hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhh....eeeee..eeeeeee...hhh.eeee..............hhhhhhhhhhhhhhhh..eeeeeee...............hhhhhhhhhhhhhhhhhhhhh...eeeeeee......hhhhhhhh....eeee....eeeehhhhhhhhhhhhhhee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------GLYCOSYL_HYDROL----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLYCOSYL_----------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cbv B   3 VKKFPEGFLWGVATASYQIEGSPLADGAGMSIWHTFSHTPGNVKNGDTGDVACDHYNRWKEDIEIIEKLGVKAYRFSISWPRILPEGTGRVNQKGLDFYNRIIDTLLEKGITPFVTIYHWDLPFALQLKGGWANREIADWFAEYSRVLFENFGDRVKNWITLNEPWVVAIVGHLYGVHAPGMRDIYVAFRAVHNLLRAHARAVKVFRETVKDGKIGIVFNNGYFEPASEKEEDIRAVRFMHQFNNYPLFLNPIYRGDYPELVLEFAREYLPENYKDDMSEIQEKIDFVGLNYYSGHLVKFDPDAPAKVSFVERDLPKTAMGWEIVPEGIYWILKKVKEEYNPPEVYITENGAAFDDVVSEDGRVHDQNRIDYLKAHIGQAWKAIQEGVPLKGYFVWSLLDNFEWAEGYSKRFGIVYVDYSTQKRIVKDSGYWYSNVVKNNGL 444
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442

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: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: (Trans)glycosidases (1191)

Family: Family 1 of glycosyl hydrolase (102)

Protein domain: automated matches (36)

Thermotoga maritima [TaxId: 2336] (20)

1a	d2cbva_	A:
1b	d2cbvb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Glycosidases (843)

Thermotoga maritima. Organism_taxid: 2336. (28)

1a	2cbvB00	B:3-444
1b	2cbvA00	A:3-446

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (BGLA_THEMA | Q08638)

molecular function
	GO:0008422	beta-glucosidase activity	Catalysis of the hydrolysis of terminal, non-reducing beta-D-glucose residues with release of beta-D-glucose.
	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.
	GO:0102483	scopolin beta-glucosidase activity	Catalysis of the reaction: H2O + scopolin <=> beta-D-glucose + scopoletin
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:0030245	cellulose catabolic process	The chemical reactions and pathways resulting in the breakdown of cellulose, a linear beta1-4 glucan of molecular mass 50-400 kDa with the pyranose units in the -4C1 conformation.
	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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Ala A:181 - Pro A:182	[ RasMol ]
		Ala B:181 - Pro B:182	[ RasMol ]
		Trp A:398 - Ser A:399	[ RasMol ]
		Trp B:398 - Ser B:399	[ RasMol ]

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

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Access by PDB/NDB ID
	2cbv
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
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	BGLA_THEMA \| Q08638
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	3.2.1.21
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1od0	FAMILY 1 B-GLUCOSIDASE FROM THERMOTOGA MARITIMA
1oif	FAMILY 1 B-GLUCOSIDASE FROM THERMOTOGA MARITIMA
1oim	FAMILY 1 B-GLUCOSIDASE FROM THERMOTOGA MARITIMA
1oin	FAMILY 1 B-GLUCOSIDASE FROM THERMOTOGA MARITIMA
1uz1	FAMILY 1 B-GLUCOSIDASE FROM THERMOTOGA MARITIMA IN COMPLEX WITH GLUCO-ISOFAGOMINE LACTAM
1w3j	FAMILY 1 B-GLUCOSIDASE FROM THERMOTOGA MARITIMA IN COMPLEX WITH TETRAHYDROOXAZINE
2cbu	BETA-GLUCOSIDASE FROM THERMOTOGA MARITIMA IN COMPLEX WITH CASTANOSPERMINE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

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