3CKB - JenaLib

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Title :   B. THETAIOTAOMICRON SUSD WITH MALTOTRIOSE

Authors :   N. M. Koropatkin, E. C. Martens, J. I. Gordon, T. J. Smith

Date :   14 Mar 08 (Deposition) - 01 Apr 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Tpr Repeat, Carbohydrate Binding, Starch Binding, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. M. Koropatkin, E. C. Martens, J. I. Gordon, T. J. Smith
Starch Catabolism By A Prominent Human Gut Symbiont Is Directed By The Recognition Of Amylose Helices.
Structure V. 16 1105 2008
PubMed-ID: 18611383 | Reference-DOI: 10.1016/J.STR.2008.03.017

Molecule 1 - SUSD
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-28A
	Expression System Strain	:	ROSETTA(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 26-551
	Gene	:	SUSD
	Organism Scientific	:	BACTEROIDES THETAIOTAOMICRON
	Organism Taxid	:	226186
	Strain	:	VPI-5482

		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	CA	2	Ligand/Ion	CALCIUM ION
2	MLR	2	Ligand/Ion	MALTOTRIOSE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MLR	1	Ligand/Ion	MALTOTRIOSE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MLR	1	Ligand/Ion	MALTOTRIOSE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:273 , GLN A:288 , ASP A:430 , ASP A:432	BINDING SITE FOR RESIDUE CA A 600
2	AC2	SOFTWARE	ASP B:273 , GLN B:288 , ASP B:430 , ASP B:432	BINDING SITE FOR RESIDUE CA B 700
3	AC3	SOFTWARE	ASP A:73 , GLU A:74 , TRP A:96 , TRP A:98 , ASN A:101 , ASN A:295 , TRP A:320 , CYS A:322	BINDING SITE FOR RESIDUE MLR A 903
4	AC4	SOFTWARE	GLN A:240 , ASP B:73 , GLU B:74 , TRP B:98 , ASN B:101 , ASN B:318 , TRP B:320 , CYS B:322	BINDING SITE FOR RESIDUE MLR B 904

(no "SS Bond" information available for 3CKB)

(no "Cis Peptide Bond" information available for 3CKB)

(no "SAP(SNP)/Variant" information available for 3CKB)

(no "PROSITE Motif" information available for 3CKB)

(no "Exon" information available for 3CKB)

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:504
 aligned with SUSD_BACTN | Q8A1G2 from UniProtKB/Swiss-Prot  Length:551

    Alignment length:511
                                    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       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550 
           SUSD_BACTN    41 SFDQQGVFVKGYAMLGVTGQKGIDGSPDLDGQDEGESGFYRTTFNCNELPTDECLWAWQENQDIPQLTSISWSPSSQRTEWVYVRLGYDITQYNFFLDQTEGMTDAETLRQRAEIRFLRALHYWYFLDLFGKAPFKEHFSNDLPVEKKGTELYTYIQNELNEIEADMYEPRQAPFGRADKAANWLLRARLYLNAGVYTGQTDYAKAEEYASKVIGSAYKLCTNYSELFMADNDENENAMQEIILPIRQDGVKTRNYGGSTYLVCGTRVAGMPRMGTTNGWSCIFARAAMVQKFFSNLEDVPMLPADVEIPTKGLDTDEQIDAFDAEHGIRTEDMIKAAGDDRALLYSGVGGGRRKIQTDAISGFTDGLSIVKWQNYRSDGKPVSHATYPDTDIPLFRLAEAYLTRAEAIFRQGGDATGDINELRKRANCTRKVQTVTEQELIDEWAREFYLEGRRRSDLVRFGMFTTNKYLWDWKGGAMNGTSVASYYNKYPIPVSDINNNRNMSQNEGYK 551
               SCOP domains d3ckba_ A: Starch u       tilization system protein SusD                                                                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------3ckbA02 A:210-307,A:412-490  [code=1.25.40.10, no name defined]                                   3ckbA03 A:308-411 SusD-like                                                                             3ckbA02 A:210-307,A:412-490  [code=1.25.40.10, no name defined]                ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.....-------...........hhhhhhhhhhhh....eee......hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhheeee.........eeeehhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh......hhhhhhh.....hhhhhh.eeeee..hhhhhh..hhhhhhhhh.................eeehhhhhh....hhhhh...............hhhhhhhhhhhh..hhhhhhhhhh.....ee................hhhhh.ee......................eeeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhh.........hhhhhhhhhhhhhh...hhhhhhhhh...........hhhhh......hhhhhh...hhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ckb A  41 SFDQQGVFVKGYAMLGVTG-------PDLDGQDEGESGFYRTTFNCNELPTDECLWAWQKNQDIPQLTSISWSPSSQRTEWVYVRLGYDITQYNFFLDQTEGMTDAETLRQRAEIRFLRALHYWYFLDLFGKAPFKEHFSNDLPVEKKGTELYTYIQNELNEIEADMYEPRQAPFGRADKAANWLLRARLYLNAGVYTGQTDYAKAEEYASKVIGSAYKLCTNYSELFMADNDENENAMQEIILPIRQDGVKTRNYGGSTYLVCGTRVAGMPRMGTTNGWSCIFARAAMVQKFFSNLEDVPMLPADVEIPTKGLDTDEQIDAFDAEHGIRTEDMIKAAGDDRALLYSGVGGGRRKIQTDAISGFTDGLSIVKWQNYRSDGKPVSHATYPDTDIPLFRLAEAYLTRAEAIFRQGGDATGDINELRKRANCTRKVQTVTEQELIDEWAREFYLEGRRRSDLVRFGMFTTNKYLWDWKGGAMNGTSVASYYNKYPIPVSDINNNRNMSQNEGYK 551
                                    50        |-      | 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       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550 
                                             59      67

Chain B from PDB  Type:PROTEIN  Length:501
 aligned with SUSD_BACTN | Q8A1G2 from UniProtKB/Swiss-Prot  Length:551

    Alignment length:511
                                    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       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550 
           SUSD_BACTN    41 SFDQQGVFVKGYAMLGVTGQKGIDGSPDLDGQDEGESGFYRTTFNCNELPTDECLWAWQENQDIPQLTSISWSPSSQRTEWVYVRLGYDITQYNFFLDQTEGMTDAETLRQRAEIRFLRALHYWYFLDLFGKAPFKEHFSNDLPVEKKGTELYTYIQNELNEIEADMYEPRQAPFGRADKAANWLLRARLYLNAGVYTGQTDYAKAEEYASKVIGSAYKLCTNYSELFMADNDENENAMQEIILPIRQDGVKTRNYGGSTYLVCGTRVAGMPRMGTTNGWSCIFARAAMVQKFFSNLEDVPMLPADVEIPTKGLDTDEQIDAFDAEHGIRTEDMIKAAGDDRALLYSGVGGGRRKIQTDAISGFTDGLSIVKWQNYRSDGKPVSHATYPDTDIPLFRLAEAYLTRAEAIFRQGGDATGDINELRKRANCTRKVQTVTEQELIDEWAREFYLEGRRRSDLVRFGMFTTNKYLWDWKGGAMNGTSVASYYNKYPIPVSDINNNRNMSQNEGYK 551
               SCOP domains d3ckbb_ B: Starch u          tilization system protein SusD                                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------3ckbB02 B:210-307,B:412-490  [code=1.25.40.10, no name defined]                                   3ckbB03 B:308-411 SusD-like                                                                             3ckbB02 B:210-307,B:412-490  [code=1.25.40.10, no name defined]                ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh..----------........hhhhhhhhhhhh....eee......hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhheeee.........eeeehhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.......hhhhhhh.....hhhhhh.eeeee..........hhhhhhhhh.................eeehhhhhh....hhhhh...............hhhhhhhhhhhh..hhhhhhhhhh.....ee................hhhhh.ee......................eeeeehhhhhhhhhhhhhhh...hhhhhhhhhhhh.........hhhhhhhhhhhhhh...hhhhhhhhh...........hhhhh......hhhhhh...hhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ckb B  41 SFDQQGVFVKGYAMLGVTG----------DGQDEGESGFYRTTFNCNELPTDECLWAWQKNQDIPQLTSISWSPSSQRTEWVYVRLGYDITQYNFFLDQTEGMTDAETLRQRAEIRFLRALHYWYFLDLFGKAPFKEHFSNDLPVEKKGTELYTYIQNELNEIEADMYEPRQAPFGRADKAANWLLRARLYLNAGVYTGQTDYAKAEEYASKVIGSAYKLCTNYSELFMADNDENENAMQEIILPIRQDGVKTRNYGGSTYLVCGTRVAGMPRMGTTNGWSCIFARAAMVQKFFSNLEDVPMLPADVEIPTKGLDTDEQIDAFDAEHGIRTEDMIKAAGDDRALLYSGVGGGRRKIQTDAISGFTDGLSIVKWQNYRSDGKPVSHATYPDTDIPLFRLAEAYLTRAEAIFRQGGDATGDINELRKRANCTRKVQTVTEQELIDEWAREFYLEGRRRSDLVRFGMFTTNKYLWDWKGGAMNGTSVASYYNKYPIPVSDINNNRNMSQNEGYK 551
                                    50        |-        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       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550 
                                             59         70

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 alpha proteins (14657)

Fold: alpha-alpha superhelix (690)

Superfamily: TPR-like (83)

Family: SusD-like (7)

Protein domain: Starch utilization system protein SusD (5)

Bacteroides thetaiotaomicron [TaxId: 818] (5)

1a	d3ckba_	A:
1b	d3ckbb_	B:

(no "Pfam Domain" information available for 3CKB)

Asymmetric Unit(hide GO term definitions)

Chain A,B (SUSD_BACTN | Q8A1G2)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:2001070	starch binding	Interacting selectively and non-covalently with starch.
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:0005983	starch catabolic process	The chemical reactions and pathways resulting in the breakdown of starch, the most important reserve polysaccharide in plants.
	GO:0005982	starch metabolic process	The chemical reactions and pathways involving starch, the most important reserve polysaccharide in plants. It is a glucan consisting of two components, amylose and amylopectin, which are both glucose homopolymers. Starch is synthesized as a temporary storage form of carbon and can be catabolized to produce sucrose.
cellular component
	GO:0009279	cell outer membrane	A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0019867	outer membrane	The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites.

Asymmetric Unit
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	Cis Peptide Bonds
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Biological Units
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	3ckb
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	SUSD_BACTN \| Q8A1G2
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UniProtKB/Swiss-Prot
	SUSD_BACTN \| Q8A1G2	:	3ck7 3ck8 3ck9 3ckc

3ck7	B. THETAIOTAOMICRON SUSD WITH ALPHA-CYCLODEXTRIN
3ck8	B. THETAIOTAOMICRON SUSD WITH BETA-CYCLODEXTRIN
3ck9	B. THETAIOTAOMICRON SUSD WITH MALTOHEPTAOSE
3ckc	B. THETAIOTAOMICRON SUSD

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Gene Ontology (9, 9)

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Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File