SAXSdb — 6kcx

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Alpha-glucosidase, putative

Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	COBALT (II) ION × 2 IMIDAZOLE × 2 ISOPROPYL ALCOHOL × 2 CITRIC ACID × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9WZL1_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–483； UniProt 1–471

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6kcx
Deposition date deposition_date	2019-06-29
Structure title title	Crystal structure of citrate complex of alpha-glucuronidase (TM0752)from Thermotoga maritima
Keywords keywords	;Hydrolase, Glycosyl hydrolase, Carbohydrate metabolism, Alpha-glucuronidase, Citrate complex, NAD(P) binding Rossman fold domain-like, LDH C-terminal domain-like, Cobalt bound ;; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6kcx__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6kcx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6kcx__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	32.40 Å
Rg (electron density)	31.82 Å
Total Rg	32.43 Å
Atom count	15050
Residues	940
Excluded volume	136500 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6kcx__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Alpha-glucosidase, putative
Molecular weight formula_weight	56895.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	7946

MGSDKIHHHHHHMKISIIGAGSVRFALQLVGDIAQTEELSREDTHIYMMDVHERRLNASYILARKYVEELNSPVKIVKTSSLDEAIDGADFIINTAYPYDPRYHDSGSQRWDEVTKVGEKHGYYRGIDSQELNMVSTYTYVLSSYPDMKLALEIAEKMKKMAPKAYLMQTANPVFEITQAVRRWTGANIVGFCHGVAGVYEVFEKLDLDPEEVDWQVAGVNHGIWLNRFRYRGEDAYPLLDEWIEKKLPEWEPKNPWDTQMSPAAMDMYKFYGMLPIGDTVRNGSWKYHYNLETKKKWFGKFGGIDNEVERPKFHEQLRRARERLIKLAEEVQQNPGMKLTEEHPEIFPKGKLSGEQHIPFINAIANNKRVRLFLNVENQGTLKDFPDDVVMELPVWVDCCGIHREKVEPDLTHRIKIFYLWPRILRMEWNLEAYISRDRKVLEEILIRDPRTKSYEQIVQVLDEIFNLPFNEELRRYYKEKL

Source Source

Source organism organism	Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
NCBI taxonomy ID ncbi_taxonomy_id	243274
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 non-polymer

Description description	COBALT (II) ION
Molecular weight formula_weight	58.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	IMIDAZOLE
Molecular weight formula_weight	69.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ISOPROPYL ALCOHOL
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	381

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d6kcxa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.0 — automated matches

Domain ID domain_id	d6kcxa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.162 — LDH C-terminal domain-like
Superfamily Superfamily superfamily	d.162.1 — LDH C-terminal domain-like
Family Family family	d.162.1.2 — AglA-like glucosidase

Domain ID domain_id	d6kcxa3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

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Unit-cell length a length_a	74.420 Å
Unit-cell length b length_b	80.410 Å
Unit-cell length c length_c	89.050 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.10 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.933 Å
Low-resolution limit resolution_low	40.205 Å
R factor r_factor	0.1432
R_work r_work	0.1411
R_free r_free	0.1843

Crystal structure of citrate complex of alpha-glucuronidase (TM0752)from Thermotoga maritima

1. Protein Identity and Related Structures Protein Identity & Related Structures

Alpha-glucosidase, putative

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6kcx__assembly_1__model_1

6kcx__assembly_1__model_1 | I(q)

6kcx__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (3 domains)

7. Citations (1)

Crystal structure of citrate complex of alpha-glucuronidase (TM0752)from Thermotoga maritima

1. Protein Identity and Related Structures Protein Identity & Related Structures

Alpha-glucosidase, putative

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6kcx__assembly_1__model_1

6kcx__assembly_1__model_1 | I(q)

6kcx__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (3 domains)

7. Citations (1)