3CK8 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   B. THETAIOTAOMICRON SUSD WITH BETA-CYCLODEXTRIN

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 :   2.10

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 (3, 16)

No.	Name	Count	Type	Full Name
1	BCD	2	Ligand/Ion	BETA-CYCLODEXTRIN
2	CA	4	Ligand/Ion	CALCIUM ION
3	EDO	10	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 1 (2, 7)

No.	Name	Count	Type	Full Name
1	BCD	1	Ligand/Ion	BETA-CYCLODEXTRIN
2	CA	-1	Ligand/Ion	CALCIUM ION
3	EDO	6	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 2 (2, 5)

No.	Name	Count	Type	Full Name
1	BCD	1	Ligand/Ion	BETA-CYCLODEXTRIN
2	CA	-1	Ligand/Ion	CALCIUM ION
3	EDO	4	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:81 , TRP A:96 , TRP A:98 , ASN A:101 , TYR A:296 , TRP A:320 , SER A:321 , CYS A:322 , GLU B:204 , GLU B:209 , TRP B:224 , LYS B:252	BINDING SITE FOR RESIDUE BCD A 800
02	AC2	SOFTWARE	ARG A:451 , ARG B:81 , TRP B:96 , TRP B:98 , ASN B:101 , TYR B:296 , TRP B:320 , CYS B:322	BINDING SITE FOR RESIDUE BCD B 900
03	AC3	SOFTWARE	ASP A:273 , GLN A:288 , ASP A:430 , ASP A:432	BINDING SITE FOR RESIDUE CA A 600
04	AC4	SOFTWARE	ASP B:273 , GLN B:288 , ASP B:430 , ASP B:432	BINDING SITE FOR RESIDUE CA B 700
05	AC5	SOFTWARE	GLU B:274	BINDING SITE FOR RESIDUE CA B 710
06	AC6	SOFTWARE	GLU A:274	BINDING SITE FOR RESIDUE CA A 720
07	AC7	SOFTWARE	TYR A:52 , GLY A:216 , ARG A:287	BINDING SITE FOR RESIDUE EDO A 730
08	AC8	SOFTWARE	GLU A:274 , ARG A:417 , PRO A:422 , ASP A:430	BINDING SITE FOR RESIDUE EDO A 731
09	AC9	SOFTWARE	ASP A:289 , LYS A:292 , GLY B:40 , PHE B:42	BINDING SITE FOR RESIDUE EDO A 734
10	BC1	SOFTWARE	GLY A:127 , THR A:131 , PRO A:174 , LYS A:176	BINDING SITE FOR RESIDUE EDO A 737
11	BC2	SOFTWARE	ASN B:318 , TRP B:320 , THR B:427 , TYR B:428	BINDING SITE FOR RESIDUE EDO B 741
12	BC3	SOFTWARE	GLY A:40 , PHE A:42 , ASP B:289 , LYS B:292	BINDING SITE FOR RESIDUE EDO B 744
13	BC4	SOFTWARE	ARG A:211 , PHE A:215 , MET A:279	BINDING SITE FOR RESIDUE EDO A 747
14	BC5	SOFTWARE	ARG B:211 , PHE B:215 , MET B:279	BINDING SITE FOR RESIDUE EDO B 748
15	BC6	SOFTWARE	ALA B:328 , GLN B:331 , LEU B:511 , TRP B:512 , ASP B:513	BINDING SITE FOR RESIDUE EDO B 749
16	BC7	SOFTWARE	LYS A:332 , GLN A:479 , ILE A:482 , ASP A:483 , TYR A:510	BINDING SITE FOR RESIDUE EDO A 754

(no "SS Bond" information available for 3CK8)

(no "Cis Peptide Bond" information available for 3CK8)

(no "SAP(SNP)/Variant" information available for 3CK8)

(no "PROSITE Motif" information available for 3CK8)

(no "Exon" information available for 3CK8)

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:501
 aligned with SUSD_BACTN | Q8A1G2 from UniProtKB/Swiss-Prot  Length:551

    Alignment length:515
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546     
           SUSD_BACTN    37 QTGGSFDQQGVFVKGYAMLGVTGQKGIDGSPDLDGQDEGESGFYRTTFNCNELPTDECLWAWQENQDIPQLTSISWSPSSQRTEWVYVRLGYDITQYNFFLDQTEGMTDAETLRQRAEIRFLRALHYWYFLDLFGKAPFKEHFSNDLPVEKKGTELYTYIQNELNEIEADMYEPRQAPFGRADKAANWLLRARLYLNAGVYTGQTDYAKAEEYASKVIGSAYKLCTNYSELFMADNDENENAMQEIILPIRQDGVKTRNYGGSTYLVCGTRVAGMPRMGTTNGWSCIFARAAMVQKFFSNLEDVPMLPADVEIPTKGLDTDEQIDAFDAEHGIRTEDMIKAAGDDRALLYSGVGGGRRKIQTDAISGFTDGLSIVKWQNYRSDGKPVSHATYPDTDIPLFRLAEAYLTRAEAIFRQGGDATGDINELRKRANCTRKVQTVTEQELIDEWAREFYLEGRRRSDLVRFGMFTTNKYLWDWKGGAMNGTSVASYYNKYPIPVSDINNNRNMSQNEGYK 551
               SCOP domains d3ck8a_ A: Starch util              ization system protein SusD                                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------3ck8A02 A:210-307,A:412-490  [code=1.25.40.10, no name defined]                                   3ck8A03 A:308-411 SusD-like                                                                             3ck8A02 A:210-307,A:412-490  [code=1.25.40.10, no name defined]                ------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.--------------.....hhhhhhhhhhhh....eee......hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhheeee.........eeeehhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.......hhhhhhh.....hhhhhh.eeeee...........hhhhhhhh.................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
                 3ck8 A  37 QTGGSFDQQGVFVKGYAMLGVT--------------DEGESGFYRTTFNCNELPTDECLWAWQKNQDIPQLTSISWSPSSQRTEWVYVRLGYDITQYNFFLDQTEGMTDAETLRQRAEIRFLRALHYWYFLDLFGKAPFKEHFSNDLPVEKKGTELYTYIQNELNEIEADMYEPRQAPFGRADKAANWLLRARLYLNAGVYTGQTDYAKAEEYASKVIGSAYKLCTNYSELFMADNDENENAMQEIILPIRQDGVKTRNYGGSTYLVCGTRVAGMPRMGTTNGWSCIFARAAMVQKFFSNLEDVPMLPADVEIPTKGLDTDEQIDAFDAEHGIRTEDMIKAAGDDRALLYSGVGGGRRKIQTDAISGFTDGLSIVKWQNYRSDGKPVSHATYPDTDIPLFRLAEAYLTRAEAIFRQGGDATGDINELRKRANCTRKVQTVTEQELIDEWAREFYLEGRRRSDLVRFGMFTTNKYLWDWKGGAMNGTSVASYYNKYPIPVSDINNNRNMSQNEGYK 551
                                    46        56 |       -      | 76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546     
                                                58             73

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

    Alignment length:515
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546     
           SUSD_BACTN    37 QTGGSFDQQGVFVKGYAMLGVTGQKGIDGSPDLDGQDEGESGFYRTTFNCNELPTDECLWAWQENQDIPQLTSISWSPSSQRTEWVYVRLGYDITQYNFFLDQTEGMTDAETLRQRAEIRFLRALHYWYFLDLFGKAPFKEHFSNDLPVEKKGTELYTYIQNELNEIEADMYEPRQAPFGRADKAANWLLRARLYLNAGVYTGQTDYAKAEEYASKVIGSAYKLCTNYSELFMADNDENENAMQEIILPIRQDGVKTRNYGGSTYLVCGTRVAGMPRMGTTNGWSCIFARAAMVQKFFSNLEDVPMLPADVEIPTKGLDTDEQIDAFDAEHGIRTEDMIKAAGDDRALLYSGVGGGRRKIQTDAISGFTDGLSIVKWQNYRSDGKPVSHATYPDTDIPLFRLAEAYLTRAEAIFRQGGDATGDINELRKRANCTRKVQTVTEQELIDEWAREFYLEGRRRSDLVRFGMFTTNKYLWDWKGGAMNGTSVASYYNKYPIPVSDINNNRNMSQNEGYK 551
               SCOP domains d3ck8b_ B: Starch util              ization system protein SusD                                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------3ck8B02 B:210-307,B:412-490  [code=1.25.40.10, no name defined]                                   3ck8B03 B:308-411 SusD-like                                                                             3ck8B02 B:210-307,B:412-490  [code=1.25.40.10, no name defined]                ------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh....--------------hhhhhhhhhhhhhhhhh....eee......hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhheeee.........eeeehhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.......hhhhhhh.....hhhhhh.eeeee...........hhhhhhhh.................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
                 3ck8 B  37 QTGGSFDQQGVFVKGYAMLGVT--------------DEGESGFYRTTFNCNELPTDECLWAWQKNQDIPQLTSISWSPSSQRTEWVYVRLGYDITQYNFFLDQTEGMTDAETLRQRAEIRFLRALHYWYFLDLFGKAPFKEHFSNDLPVEKKGTELYTYIQNELNEIEADMYEPRQAPFGRADKAANWLLRARLYLNAGVYTGQTDYAKAEEYASKVIGSAYKLCTNYSELFMADNDENENAMQEIILPIRQDGVKTRNYGGSTYLVCGTRVAGMPRMGTTNGWSCIFARAAMVQKFFSNLEDVPMLPADVEIPTKGLDTDEQIDAFDAEHGIRTEDMIKAAGDDRALLYSGVGGGRRKIQTDAISGFTDGLSIVKWQNYRSDGKPVSHATYPDTDIPLFRLAEAYLTRAEAIFRQGGDATGDINELRKRANCTRKVQTVTEQELIDEWAREFYLEGRRRSDLVRFGMFTTNKYLWDWKGGAMNGTSVASYYNKYPIPVSDINNNRNMSQNEGYK 551
                                    46        56 |       -      | 76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546     
                                                58             73

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	d3ck8a_	A:
1b	d3ck8b_	B:

(no "Pfam Domain" information available for 3CK8)

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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	3ck8
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	SUSD_BACTN \| Q8A1G2
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UniProtKB/Swiss-Prot
	SUSD_BACTN \| Q8A1G2	:	3ck7 3ck9 3ckb 3ckc

3ck7	B. THETAIOTAOMICRON SUSD WITH ALPHA-CYCLODEXTRIN
3ck9	B. THETAIOTAOMICRON SUSD WITH MALTOHEPTAOSE
3ckb	B. THETAIOTAOMICRON SUSD WITH MALTOTRIOSE
3ckc	B. THETAIOTAOMICRON SUSD

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 16)

Sites (16, 16)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Gene Ontology (9, 9)

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